I'm elevating (and reworking a little) some of the content of my own comment on the other thread, since I think this is an important thing to try to get clear. The point is that neither the "New Atheism" nor an anti-accommodationist approach to the relationship between religion and science entails being gnasty.
The point of the "new Atheism" was never to act in a way that is in-your-face, nasty, uncivil, etc., such as "Tom Johnson" notoriously described in one of the recent internet debates. Likewise, the anti-accommodationist position was never that we should go around acting like that. By acting in a civil way towards religious people, at least when those people are themselves civil, Jerry is in no way abandoning his support for the work of, say, Richard Dawkins. Nor is he becoming an accommodationist.
To the extent that there is something worth calling the New Atheism it is about criticising religion in the sphere of popular discourse - in books aimed for a wide market, in newspapers, in television appearances, etc. - and not just in academic journals and books written for academics. That is what changed last decade. It is about a forthright and popular atheism, but it is not about being literally aggressive. You can say, I suppose, that there's a sense in which it involves marketing atheism in an "aggressive" way - in the same sense that any other "product" can be marketed "aggressively" (in inverted commas). I.e., resources will be thrown at it. It will be made a priority, with an investment of energy to attract people's attention. But the New Atheism was never about literal aggression in the sense of being downright uncivil or nasty. This is part of the reason why the Tom Johnson story was so implausible. No one ever told people that they should behave in the way that "Johnson" described.
The anti-accommodationist aspect of some of our thinking is, as others are saying, about whether there is a place for religion within a scientific view of the world (or how far a scientifically-informed understanding of the world can accommodate religion). The idea has never been to claim that it is just impossible to find an arguably religious position that is at least formally consistent with science. Examples are a very austere kind of Deism and a highly non-literalist viewpoint that explains claims about supernatural events as metaphors.
Those of us who identify as anti-accommodationist don't deny that such positions exist. Our point is more that science tends to push thoughtful religious people into such positions rather than traditional positions that involve, say, a providential God and various supernatural events. (And, I now add, there is then a set of issues as to why the austere Deist or non-literalist views, which leave out much that made religion psychologically attractive in the first place, should be taken seriously.)
What we do say is that it's hopelessly misleading to go around saying "Science and religion are compatible." It would be more true to say that science tends to undermine all or most traditional forms of religion, making them less plausible, putting pressure on the religious to thin out their supernaturalist, providentialist views of the world, and so on. The result is that much in the way of actual religion really is threatened by the advance of science. Claiming otherwise is, we say, likely to be disingenuous (or, to be fair, simply mistaken).
We then have a great deal to say about the various ways in which science does this. In particular, we tend to criticise ideas such as NOMA, which seem to us to be full of problems. For example, NOMA gives a characterisation of religion that is totally untrue to the historical experience of the phenomenon.
None of this is about acting in ways that are uncivil.