tbh anders as a religious character and indeed religion being a deeply important thruline in da2 is compelling 2 me bc yes The Chantry as an institution is bad. full stop. but anders doesn't blow up the chantry bc he hates andrastianism — the way he talks abt andraste indicates that he admires her, that he's trying to emulate her, even, that he doesn't think she would appreciate what's been done w her teachings re: mages. he believes himself to be adhering to a truer version of andrastianism, and tbh i think from there it can be p easily extrapolated that he doesn't consider blowing up the chantry to be a desecration so much as a purification. by fire!
he also lives in darktown, where ppl openly complain abt having been abandoned by the chantry. in the context of a religion where the maker has abandoned EVERYONE, i think that's way more loaded than even the accusation of hypocrisy that potentially resonates w the player.
i like that in awakening, he expresses explicitly that he thinks abt andraste as a real person who really existed. to me, that casts his sexual comments (lmao) towards andraste as both a kind of annoying, passive aggressive way of yanking the rug out from under anyone who gets too precious abt andraste and also, yeah, he says sexually annoying things to needle ppl.
i think a lot of faithful andrastians might have a v difficult time praying in a chantry like the one in hightown. but esp for someone like anders, who is in over his head trying to take care of all the ppl that specific chantry has abandoned, like. the religious vibes of that are v compelling to meeeeeeee.