The are two issue to bring up here (from IEP)
(1) you seem to assume that Bacon's visions of science is what happens in reality. Some beg to differ e.g.:
[Bacon's method proposals made] the English physician (and neo-Aristotelian) William Harvey, of circulation-of-the-blood fame, to quip that Bacon wrote of natural philosophy “like a Lord Chancellor” – indeed like a politician or legislator rather than a practitioner. The assessment is just to the extent that Bacon in the New Organon does indeed prescribe a new and extremely rigid procedure for the investigation of nature rather than describe the more or less instinctive and improvisational – and by no means exclusively empirical – method that Kepler, Galileo, Harvey himself, and other working scientists were actually employing. In fact, other than Tycho Brahe, the Danish astronomer who, overseeing a team of assistants, faithfully observed and then painstakingly recorded entire volumes of astronomical data in tidy, systematically arranged tables, it is doubtful that there is another major figure in the history of science who can be legitimately termed an authentic, true-blooded Baconian. (Darwin, it is true, claimed that The Origin of Species was based on “Baconian principles.” However, it is one thing to collect instances in order to compare species and show a relationship among them; it is quite another to theorize a mechanism, namely evolution by mutation and natural selection, that elegantly and powerfully explains their entire history and variety.)
Science, that is to say, does not, and has probably never advanced according to the strict, gradual, ever-plodding method of Baconian observation and induction. It proceeds instead by unpredictable – and often intuitive and even (though Bacon would cringe at the word) imaginative – leaps and bounds. Kepler used Tycho’s scrupulously gathered data to support his own heart-felt and even occult belief that the movements of celestial bodies are regular and symmetrical, composing a true harmony of the spheres. Galileo tossed unequal weights from the Leaning Tower as a mere public demonstration of the fact (contrary to Aristotle) that they would fall at the same rate. He had long before satisfied himself that this would happen via the very un-Bacon-like method of mathematical reasoning and deductive thought-experiment. Harvey, by a similar process of quantitative analysis and deductive logic, knew that the blood must circulate, and it was only to provide proof of this fact that he set himself the secondary task of amassing empirical evidence and establishing the actual method by which it did so.
One could enumerate – in true Baconian fashion – a host of further instances. But the point is already made: advances in scientific knowledge have not been achieved for the most part via Baconian induction (which amounts to a kind of systematic and exhaustive survey of nature supposedly leading to ultimate insights) but rather by shrewd hints and guesses – in a word by hypotheses – that are then either corroborated or (in Karl Popper’s important term) falsified by subsequent research.
(For a [much] more sympathetic view towards Bacon in this regard, see SEP.)
(2) it's Bacon's view of the humanity-nature relationship that's usually criticized
(and his view of science was basically subordinate to that):
Bacon’s reputation and legacy remain controversial even today. While no historian of science or philosophy doubts his immense importance both as a proselytizer on behalf of the empirical method and as an advocate of sweeping intellectual reform, opinion varies widely as to the actual social value and moral significance of the ideas that he represented and effectively bequeathed to us. The issue basically comes down to one’s estimate of or sympathy for the entire Enlightenment/Utilitarian project. Those who for the most part share Bacon’s view that nature exists mainly for human use and benefit, and who furthermore endorse his opinion that scientific inquiry should aim first and foremost at the amelioration of the human condition and the “relief of man’s estate,” generally applaud him as a great social visionary. On the other hand, those who view nature as an entity in its own right, a higher-order estate of which the human community is only a part, tend to perceive him as a kind of arch-villain – the evil originator of the idea of science as the instrument of global imperialism and technological conquest.
On the one side, then, we have figures like the anthropologist and science writer Loren Eiseley, who portrays Bacon (whom he calls “the man who saw through time”) as a kind of Promethean culture hero. He praises Bacon as the great inventor of the idea of science as both a communal enterprise and a practical discipline in the service of humanity. On the other side, we have writers, from Theodor Adorno, Max Horkheimer, and Lewis Mumford to, more recently, Jeremy Rifkin and eco-feminist Carolyn Merchant, who have represented him as one of the main culprits behind what they perceive as western science’s continuing legacy of alienation, exploitation, and ecological oppression.
IEP here is actually being fairly biased in that the list of Bacon hagiographers is fairly long as well, even in recent times; the SEP entry is basically almost a polar opposite--e.g. Urbach is quoted umpteen times on the SEP page (and none at all on IEP.) Likewise for: Rees, Gaukroger and Pérez-Ramos (Gaukroger is the only one of these even mentioned on IEP's page, and only as "further reading" but not cited for anything.)
As far as witches and Bacon.... that's probably a stretch.
What other commentators, e.g. Serjeantson (2014) have pointed out in Bacon's terminology is that he
(almost certainly due to his legal career) uses certain legal terms in the
realm of science and philosophy; the chief one seems to be "indicium" (but also "inquisitio" appears).
What is an indicium? Like “interpretatio,” the term does not appear in Goclenius’s
specifically philosophical lexicon. But it does appear in several legal lexicons of the late
Renaissance, including those of Pardoux Duprat and Simon Schard, where it is defined as
“a sign . . . of a crime, or of something else that is sought . . . an aid to proof.” Perhaps
the foremost theorist of legal indicia in Bacon’s time was Jacopo Menochio (1532–1607),
who treated them at length in his massive Commentary on Presumptions, Conjectures,
Signs, and Indications (1587–1590). Menochio endorses the association we have already
seen between indicia as the grounds for inquisitio. He also offers a full account of what
indicia are. Following the authoritative commentator Baldus de Ubaldis, Menochio
distinguishes between a “half-full” (semi-plenum) indication—a form of presumption that
“strongly moves the mind to credit or discredit something”—and a “full” (plenum)
indication, which is even better, for it is “the demonstration of a thing by a different sign,
by which the mind relies on something just as if it existed.”
This is not to argue that Bacon’s own philosophical doctrine of indicia vera is
straightforwardly that of the civilians. But his use of their terminology provokes the strong
suspicion that he is developing his ideas about “inquisition,” “indication,” and ultimately
perhaps even “interpretation” from the civilian law of evidence. Moreover, to this
developing web of legal terminology in Bacon’s philosophy of science we can add a
further node, which we also encountered at the beginning of this account: the persistent
references in Bacon’s unpublished early writings to a “formulary” or formula of interpretation. A formularius in late medieval Latin was precisely a “lawyer who was skilled
in formulae,” and formulae in the law that Bacon knew were the set terms in which
indictments or actiones were brought against those charged with crimes.
So it seems uncontroversial enough to say that Bacon couched his scientific
method in semi-legal terminology, or at least terminology inspired from the domain of legal evidence (gathering).
As to one more obscure connection:
There is, finally, a little-noticed passage in one of Bacon’s unpublished writings that
might clinch this case for a legal origin for the interpretatio naturae. In the volume of
Writings in Natural and Universal Philosophy (1653) that Isaac Gruter printed from the
manuscripts supplied to him by Bacon’s executor William Boswell (d. 1650) there appears
a little-studied treatise entitled Filum labyrinthi, sive inquisitio legitima de motu. In this
short treatise Bacon makes a rare explicit analogy between legal processes and the study
of nature: “Just as those civil judgments are most incorrupt and honest where least oratory
and obfuscation (or even eloquence) is condoned, but instead almost all the time and effort
is employed on witnesses; so, in the same way, the best judgments about Nature are
achieved when things are deduced by numerous and evident testimonies of experience,
rather than by the presentation of aggressive or plausible speeches or disputations.” The
“testimonies of authors,” Bacon goes on, are bound up with desires and inducements; but
the “testimonies and answers” of things, though they are sometimes cryptic and obscure,
are always sincere and uncorrupted. This passage does not explicitly invoke the idea of
“interpretation.” But it does suggest very strongly that Bacon’s vision of natural investigation had its origin in the processes of legal inquisitio. If this is so, then Bacon’s general
theory of the “interpretation of nature” may perhaps also be regarded as having a
significantly legal foundation. [...]
Before Bacon’s intervention, it appears that “interpretation” was not in fact an activity
practiced upon nature either by natural philosophers, or by learned Galenic physicians, or
by their Paracelsian counterparts, or by natural magicians, or even by alchemists. They
preferred to conceive of their natural investigations in terms of cognition, explanation, and
analysis, not in terms of the textual procedure of “interpretation.” [...]
By contrast, in the realm of law we have found a number of suggestive parallels
between specifically civilian legal procedures and the terminology that Bacon associates
with his idea of interpreting nature. Not only Bacon’s use of interpretatio itself, but also
the closely associated concepts of indicia, inquisitiones, and formulae, seem to have their
origins in the law.
Serjeantson goes as far to suggest that this (then novel) use of legal terminology in philosophy by Bacon may have had something to do with the retorts that his work received (including the one by William Harvey, mentioned further above.)