Professional history of science has spent the last century taking the conflict thesis apart, and the demolition is not a minority view. The objections are of several kinds and they compound.
The first is that the categories are anachronistic. Before the nineteenth century there was no profession called science standing over against something called religion; there were natural philosophers, most of them clergy or funded by the church, working inside institutions that saw no boundary to defend. The second is that the standard episodes do not behave as the thesis needs them to. The Galileo affair turns out on the documents to involve patronage, personal insult, Aristotelian university faculties defending their turf and a pope who had been an admirer, rather than a straightforward collision between observation and dogma. The third is that several of the thesis's best known illustrations are simply untrue, and were untrue when they were published.
Historians who reject the warfare model do not replace it with harmony. The preferred term is complexity: the relation has been one of conflict, of independence, of dialogue and of active sponsorship at different times and in different places, sometimes simultaneously in one person. That is a harder story to tell in a sentence, which is a large part of why the warfare version survives in popular argument long after the field that studies it abandoned the model.