As far as I can tell it was mostly due to overreaction of scientific establishment that baffled the moderately religious (here including even the previous Pope, who didn't have any problem with evolution as such, only with people using it to oppose their beliefs) have religious nutjobs managed to get the moderates on board and reach so much influence here.

I don't think the religious nutjobs have managed to get the moderates on board. Following the alteration of science curricula by evangelicals the public has consistently elected moderates who then removed ID from classrooms- plausibly this had something to do with science putting up a unified front against ID. I don't know how we can reliably compare this world to a counter-factual one in which science doesn't have the siege mentality. But it seems plausible that in such world the position of science would be more precarious.

But the ID issue aside, do you not think that, in general, powerful and influential fundamentalist movements will be bad for science? You've got around 40% of the American public that doesn't believe in evolution (though of course this varies by how the question is asked) and it seems reasonable to believe that the larger that group is the more at risk high school biology curricula is.

I don't this it would be right to ignore this, as this unreasonable siege mentality is a major impediment to fixing science.

This seems like putting the cart before the horse. Is there even an organized programme for reform around for the establishment to resist? While I think the siege mentality makes people wary of criticizing science I also think there plenty of ways to do so without especially undermining science visa vis religion. I think the successes of the more radical factions of the two American political parties is an illustrative analogy though obviously not the ideal inspiration for science reform.