I cant speak to the reception that this got at the time but an important factor is that Claremont was careful not to demonize or misrepresent religion as a whole or the religious themselves in the process. He makes a point to represent religious tolerance as well as have positive religious characters who the reader can relate to in Kurt and Kitty. So anyone who is religious is less likely to have a knee jerk response and can see that he is separating mainstream Christianity from toxic Christianity or maybe whats more accurately a "mis-use" of Christianity.
I feel like this is what a lot of writers are failing to do right now so you have instances where readers feel like the bad guy is made to represent them despite their more normal/tolerant positions. I dont think anyone reaching for an XMen comic relates to the politics of Stryker but its important for the writer to understand that and translate that understanding to their audience so they arent left there thinking "wait is this Stryker character supposed to be me?!? F___ You Claremont!". Which is really a message that needs to be related well to the entire audience if the story is to open a positive dialogue.