I understand your concern here, but in fact philosophy and theology are all about how we can arrive at higher truths and Truths.
Science, in effect, says: that's not our concern, all we really care about is: natural explanations for natural processes.
We'll leave "truth" or "Truth" to other disciplines.
Now, when people use their understandings of truth/Truth to "prove" that science is not only wrong, but wicked, then science can only suffer such crucifixions in silence, and hope that the future will treat them better.
Science itself has no defense against such "truths" except, well, more & better science.
Well, I'm not "science". I don't have to quietly accept that those tactics and that level of discourse must be allowed to stand, and go unchallenged.