like ba@, i would fight those attitudes when i come across them, regardless of who/what/where.
i would not try to stop an anti-liberatory institution that is built upon discrimination from some subset of its discriminations; i would rather see that institution destroyed. as an anarchist, i would not waste my time on either the action (reform) or the target (religion).
on the other hand, if the target of the discrimination is not a follower of (the discriminatory) religion, all bets are off, and any action taken by the target (and allies) in defense may be appropriate. especially if the target is an anarchist! ;-)
if folks who believe in and are part of that institution care to fight the institutional hierarchy in order to stop some specific discrimination, i say have at it! i hear there's a downright liberal in the vatican these days.