Your concern is reasonable and is the best argument for visiting St. Bonaventure. Websites can only tell you so much… however, definitely recommend that you look at the curriculum requirements at both schools. Many Catholic colleges will let students take standard (non-religious) philosophy courses to meet the Theology/Philosophy requirements. Dig deep into that aspect at both Canisius and SB, because that is where he is likely to be expected to discuss religious issues.
Canisius and St. Bonaventure are not considered to be religiously conservative, and my guess is that neither one would make your son uncomfortable. The kind of school your family really wants to avoid is Franciscan University of Steubenville (hint @collegeparentnew SB is not the only Franciscan university in the US). Steubenville has lots of folks who are “more Catholic than the Pope.”