I suppose Marx (if brought suitably up to date) would reply that the downside of driving some people away would be more than compensated by the upside of liberating some people from their religious delusions and thus enabling them to think more clearly about existential risk.
(I've no idea whether he'd be right.)
There's a comment from one of the people responsible for the Sequences ebook, arguing that it wouldn't be feasible to remove all the anti-religious material and speculating on whether re-ordering what's there might make it less of an immediate turn-off for religious readers.
As a religious person myself, I have to say that's the one part of the Sequences that seems to me to be poorly fitted. (I haven't read them all, but in the ones I have read). Its inclusion seems to follow one of two patterns.
The first pattern is, "all religion is false and I do not have to explain why because it is obvious". These I ignore, as they give me no information to work from. (Your use of the phrase "religious delusions" I also class under this category).
The second pattern is, "I have known religious people who have fallen...
Another month, another rationality quotes thread. The rules are: