In order to answer this question as stated in the penultimate paragraph, we must first show how a lowering of the burden of proof to a preponderance of evidence constitutes an infringement of the presumption of innocence. Paul Roberts argues that there are three reasons for this (but I only see two and will present them as such for ease). The first is that in cases of doubt the void where evidence is lacking must be filled by a presumption. This means that in cases which require the defendant to prove innocence they must 'convince' a judge/jury which necessitates, so Roberts argues, a presumption of guilt prior to such an argument being made. The second (and third) basically both argue that because the resources of the state/official body are so much greater than those of the defendant, the burden of proof should rest with them as they are the most likely to be able to find it, any other situation would allow that the defendant were less well equipped and so amount to a presumption of some wrong-doing that would justify such otherwise unfair treatment.
I think it might also help to briefly outline the way in which philosophers of law talk about guilt and innocence as there has been some confusion in the other answers. To be guilty of an offence legally obviously means that one has done something which the law prohibits, but in order to justify that law morally, it is necessary that one has committed some moral wrong. The problem then is how to define moral wrong, separate to legal wrong, in any objective sense. The way this is done is by saying that the moral wrong (as opposed to the legal one) is that which transgresses the type of activity the law intended to avoid by its enactment. For example, the speed limit is not intended to control the speed of cars for their own sake, it is intended to avoid dangerous driving, someone driving over the speed limit but (perhaps by reason of their superior skill) doing so entirely safely will have committed a legal wrong but be morally innocent.
In the example above, the speed limit is a practical way of reducing dangerous driving, it does not interfere with the presumption of innocence, however, because there is not room for doubt (as explained above). Some laws, however, called divergent offences (after Tadros) can be argued to interfere with presumption of innocence and the example in the OP is just such a rule. So, these offences are ones where the offence is in the form "committing X without having sufficient proof of Y", here 'sufficient' proof might be only more than 50%. It is still required that the offence must be proven beyond all reasonable doubt (satisfying Roberts), but the offence itself is that of 'not possessing sufficient proof'. In some cases this have been justified;
Where the intention of the law is to provide assurances. For example
in workplace safety an employer could be prosecuted for failing to
have checked a safety item merely on a preponderance of evidence,
thus the employer might actually be innocent of 'causing harm to an
employee' in the sense that they did not intend to do so (49%
chance), but "The employer’s duty is not just to provide, but to
‘ensure’ that she provides, a workplace that is, as far as is
reasonably practicable, safe" (Duff 'Strict Liability, Legal
Presumptions, and the Presumption of Innocence').
Where it would be so incumbent on the accused to have secured proof
that they were morally in the right, that such proof should be
easily to hand (thus reversing the second of Roberts' reasons not to
shift the burden of proof). This is the argument used in sexual
offences such as in the OP. If one intended to have intercourse with
someone who was inebriated or even semi-concious, the reasonable
efforts one could be expected to take to ensure consent had been
given would be so evident that they (rather than the prosecution)
would have the easier burden proving consent.
Where proof of some activity p implies (without cause for
rebuttal) some intent q. Here, technically the accused is being
'presumed guilty' of the offence simply by virtue of having engaged
in some related activity. This is usually justified where q is
difficult to prove, but p always leads to q in all
circumstances. An example is murder, which necessarily requires
intent to kill (or reckless lack of concern). This can be simply
'presumed' from the activity of waiving a knife at someone's throat,
as it is clear that such an action might lead to their death. The
accused can be 'presumed guilty' of intent without any evidence at
all of their intention, simply by inference from their action.
Where we might have reason to criminalise something on the grounds
that it regularly causes harm, but for practical reasons we only
criminalise the actual harm. In such cases the person carrying out
the activity might justifiably be 'presumed guilty' of doing so
recklessly and so guilty of harm with intent. This might also
pertain to the example in the OP, where one might reasonably criminalise
all sexual activity without clear consent, it would be impractical
to do so, but it would not be unfair in those cases where harm has
been caused, to presume recklessness on the part of the person who
does not have ready proof of consent to hand.
- Issues of legal guilt can be issues of moral guilt where one examines
the intent of the law.
- Placing a lower burden of proof of the accused can constitute a shift
in the presumption of innocence because it can put the accused at an
unfair disadvantage which would not be justified unless they were
presumed first to be likely guilty.
- Such shifts in presumption can be morally justified in cases where,
for various reasons, the activity the law intends to prohibit is one
of "doing X without possessing a preponderance of evidence of Y"
Justification therefore rests on whether a greater harm is done to society by people engaging in X without proof Y, than the burden on the individual of having to obtain Y before every X. In this we must remember that most moral justifications for the interference in personal freedoms are that doing so is necessary to secure the rights of others, so the question is essentially, could the rights of the potential victims here be protected by any other means? If they could, then the shift in presumption is not justified, if they could not, then it is.