Richard Dawkins has been asking straightforward yet deep questions about matters of intense emotional salience (to some) for as long as he's been in the public eye as an atheist.

In this way, Richard Dawkins has been undermining organized religion since forever. He is perhaps the most prominent face of "New Atheism"--not reticent or apologetic about calling out nonsense-as-they-see-it in religion. No "two spheres of influence" thing, no sugar-coating. Just: religions don't make sense, and they're wrong and harmful. Dawkins has said all sorts of stuff about organized religion...and of course all these things have had much rebuttal directed at them prior to his saying of it. And if you're expecting tact...well...no, that's the New Atheists' style too--to the consternation of other atheists who preferred a more reflective approach.

I'm not sure why you'd expect anything different from him in this case. Dawkins' points are at times oversimplified to the point of wrongness, but this "how dare he!" type response is ridiculous. That's exactly the kind of thing that New Atheists attack most stridently: orthodoxy and shaming instead of debate and discourse. If any movement starts seeming more ideology than rationality, if their arguments seem infused with hypocrisy and internal contradictions, and social pressure rather than argumentation is used to produce conformity, I would expect to see people like Dawkins wade in. As he wrote in The God Delusion, "I do everything in my power to warn people against faith itself, not just against so-called 'extremist' faith."

The proper way to respond to a New Atheist-style attack is to answer the question. Answer it well. With data, with assumptions clearly specified, and impeccable logic...or at least admit the flaws, weaknesses, and point to where further work needs to be done.

The problem that theists have had is that they actually end up not having particularly compelling answers to things like the problem of evil. So Dawkins will point out something like, I don't know, river blindness, and theists reply with appeal to mystery, or absolutely rubbish biology, or some long transcendental argument that itself has pretty trivial flaws. The New Atheists are (mostly "were"; they're not much in the public eye nowadays) constant thorns in the side of organized religion, mostly because religions can't actually answer the question.

If other things start feeling like organized religion ("the Son, the Father, and the Holy Ghost are three persons in one indivisible Godhead, and don't you dare ask how that's even a coherent concept, let alone try to deny it!"), you should expect the seeming-ideology to be jabbed and prodded. But if you happen to be correct, just give good answers!

Anyway, this is absolutely 100% on target for classic Dawkins, and therefore gives zero information about whether he's speaking in "bad faith" (the pun, applied to perhaps the world's most famous atheist, is hilarious).

There might be other statements he's made that provide some insight as to his feeling about trans people (if that's relevant), but this one only reaffirms that Dawkins is still Dawkins.