To me, the main goal of hermeneutics is to derive the meaning of the text as it was originally intended by the author. So, no, we do not have to necessarily say that just because one part is a metaphor, or is meant to be taken allegorically, that it follows the rest be taken in a similar fashion, for it may have been the case the original author intended only part of their writing to be taken metaphorically, while other parts to be taken literally. If the original author didn't, or couldn't have intended a certain part as a metaphor, I see no reason taking that part to be one as valid, so it isn't the case that one must say just because one part is a metaphor, it is a valid position to take the rest as a metaphor.
Another problem is assuming that it must be taken exclusively as literal or metaphorical. Multiple rabbis and church fathers thought it was both, and had a dual significance. For example, Ramban in his commentary to Genesis 3 wrote this:
“You should know that and believe that the Garden of Eden is a real place on earth, and that there are still in it the Tree of Life and the Tree of Knowledge...”
But in the same comment, he later wrote:
“...Now, if the Tree of Knowledge was 'good for man, for eating and desirable for him as a means of awareness (3:6)', why did God withhold it from him? For God is good and benevolent; “He does not withhold good from those who walk in innocence! (Psalms 84:12) Furthermore, the serpent today has no “soul of speech”, so how was it able to speak in the manner that it did? And if you say that it did originally have the power of speech, but that power was removed as part of its punishment, scripture should have mentioned in the description of the curse that his mouth would now be silenced, for this would be the most severe of all the curses! Rather, all of these events in the story have dual significance, and both the apparent and hidden meanings in them are true.”
Also, it is hard to determine exactly where we draw the line for what constitutes a metaphor and what doesn't. For example, does idiomatic language constitute a metaphor? If it does, then the Bible has to be taken metaphorically to some extent, since both Koine Greek and Biblical Hebrew were highly idiomatic languages. An example of this could be in Genesis 4:1, where it says:
“והאדם את חוה אשתו”
“And the man knew his wife”
Taken literally, the verse makes little sense, since it should already be clear that Adam knew his wife. But, given the juxtaposition between “conceived” and “bore”, and the fact that it is used in other verses to mean “have sexual relations with”, we can reasonably assume it means the same thing here.
Another example that's used fairly commonly is one as in Exodus 32:19, where it says:
“יחר אף משה”
“And the anger of Moses burned.”
This literally doesn't mean there was, in a literal sense, the “anger of Moses”, which literally burned with literal fire. It means he was mad.
A last example could be בני מת
“sons of death.” It is not used to mean literally that there are literal sons of someone named “death”, but that the people being talked about are sure to die.
If these constitute metaphors, then it isn't even possible to take the Bible literally and have it make sense.
If it isn't the case that you take idiomatic language to be a metaphor, saying something like even though the idiom is not to be read at face value, once the meaning of it is derived, that is to be taken literally, then I think we can still make a case that it isn't inconsistent to take part of the anthology of books we have as a metaphor, while taking other parts literally. The question I think we should always ask is what the intent of the author was, and how should we understand what we're examining, given the culture and time it was written in. Giving a general answer to this question is very hard, so I will use the case of the Genesis account.
Many think the Genesis account has similarities with Near Eastern Cosmogonies.
For example, It was common among those of the Near East to think the primordial substance was water, and the primordial substance in the Genesis account is water.
It was also common in the Near East to see serpents as objects of fear and worship, and so it is an object of fear in this story. In the tradition of the Sumerians, we have the myth of Enki and Ninhursag, which talks about paradise lang similar to the garden of Eden. Furthermore, some have maintained that the garden itself was an already established tradition, in order to explain the problems we come across when dealing with the verse in Ezekiel which talks about the “garden of God.”
We also have the use of “sea monsters” in Genesis, which were common devices as well, and we have different accounts of creation where God fights giant sea monsters in order to create the earth (which was the theme of stories like the Enuma Elish). In order to see this, check Psalms 74:13 and Isaiah 51:9 or Proverbs 8:22 – 31.
Another motif is the tree of life, which can be seen to be similar as the “plant of life” in Babylonian Mythology.
There is also the fact that man was created from the ground only after it rains in Genesis 2:5, and the fact that similar substances were used to create humans in other cultures. In Egypt, the God Khnum made living creatures on a potter's wheel, and in Babylon the wild man Enkidu was made from clay.
If someone was combining various existing traditions, it is hard to see how they'd understand what they made as literal in any sense. So, most people take this as an indicator that the account we have is a statement of faith, which common motifs to express theological beliefs. If true, we have evidence not to take it metaphorically, and since it is a statement of faith, God is not a metaphor in it.
This is a debatable point though, so I don't think it's sufficient enough to establish a case. If someone disagrees with this point, I think we can still make a case using internal evidence.
The first thing we notice is the repetition. In every verse we have,
"ויאמר אלוהים יהי
"and God said let there be"
"and it was so"
"and God created"
"וירא אליהים כי טוב’
"and God saw that it was good"
We do not see this in historical accounts.
We also have multiple verses using synonymous parallelism, which is used in Hebrew poetry. It is when two words are used in conjunction to refer to the same idea. Here are some examples outside of Genesis:
"יהוה הצילה נפשי משפת–שקר לשין רמיה"
"Save me Lord, from lying lips and deceitful tongues" – Psalms 120:2
This is an instance of synonymous parallelism. "Lying lips" and "deceitful tongues" refer to the same thing.
Another instance is the famous passage in Isaiah 53.
"והיא מחלל מףשענו מדכא מעונורינו"
"He was wounded from our transgressions, and was crushed from our iniquities." Yet again, "wounded from our transgressions" and "crushed from our iniquities" are both referring to the same thing, so this is an instance of synonymous parallelism.
Keeping this in mind, we can read the text in Genesis and see multiple instances where this occurs:
"והארץ היתה תהו ובהו"
"and the earth was formless and void" - Genesis 1:2
"ויאמר אלוהים תדשא הארץ דשא עשב מזריע זרא"
"Let the earth bring forth vegetation, plants sowing seed" - Genesis 1:11
"ויברך אתם אלוחים לאמר פרו ורבו"
"Be fruitful and multiply" - Genesis 1:22
"ויאמר אלוהים נעשה אדם מצלמנו וכדמותנו"
"And God said, 'Let us make man in our image, after our likeness" - Genesis 1:26
"ויכל אלוהם ביום תשביעי מלאכתו אשר עשה וישבת ביום השביעי מכל מלאכתו"
"On the seventh day God completed the work that he had done, and on the seventh day he rested from all the work that he had done" - Genesis 2:2
"ויברך אלוחים את יום השביעי ויקדש"
"He blessed the seventh day and sanctified it" - Genesis 2:3
"זאת הפעם עצם מעצמט ובשר מבשר"
"This time it is bone from my bones and flesh from my flesh" - Genesis 2: 23
We can also take note of the fact that there are a couple of verses, which can be seen as having intentional poetic wordplay.
In Genesis, 2:25, the text says:
"ויהיו שניהם ערימים"
"and both of them were naked"
The Hebrew word for "naked" is ערם and shares the same root as the word for "cunning" in Genesis 3:1. Many have thought it to be poetic wordplay.
We also have a similar instance in Genesis 3:20:
"ויקרא האדם שם אשתו חוה כי הוא היתה אם כל חי"
"The man called the name of his wife 'Eve', for she was the mother of all living"
Eve in Hebrew is חוה (chavah), which is derived from the verb "to live", and "living" here is חי (chay), which comes form the same root. She is called chavah as poetic set up to establish chay later in the verse.
As a matter of fact, the Septuagint (a famous Greek translation of the old testament) translates the verse like this:
“και εκαλεσεν Αδαμ το ονομα τησ γυναικοσ Ζωη, οτι αυτη ματηρ παντων των ζωντων”
“And Adam called the name of his wife “life”, for she was the mother of all living.
We can also make a similar case for Adam's name, since אדם "Man (adam)” shares the same root as אדמה "ground (adamah)” and he “was formed from the dust of the ground.”
Lastly, they are never called definite names. The story consistently refers to the characters as האדם "the man” and האשח "the woman.” The verses which are usually translated as calling them definite names can be seen as poetic wordplay.
From this, I think at the least, it is reasonable to suppose that some of this account was intended to be taken allegorically. Assuming it is taken metaphorically, with the use of poetic language and common motifs, the question becomes to what extent we take it metaphorically. This requires putting it further into its context, since it would be hard to make a case that an ancient text has concept x when concept x wasn't even developed during the time it was written. We have no evidence to suppose God was worshipped as a metaphor, we have ancient civilizations who relied on the worship of their god(gods usually) to influence the world around them, to bring about rain, to bring a good harvest, and so on. That assumes that they are real character with a real influence on the real world. It would be hard for us to make the case to suppose that “God can be taken as a metaphor, if some of the text is taken as a metaphor”, when “God as a metaphor” wasn't a coherent concept at the time it was written (or at least, there is no evidence I know of that it was one). However, if we take into account the language and concepts used, we can see some of it was not meant to be taken literally.
So no, it is not dishonest to take only part of a story as literal or as metaphorical, so long as you have a valid criteria to distinguish where to draw the line. In this case, I think we do have one. The only time it becomes dishonest is when you are not consistent in doing so, or consciously denying evidence which leads you to the opposite conclusion you are holding.