Certainly balancing Charter rights is what drives the case..  The Ontario courts basically found that TWU has a religious right to run a law school but that doesn't mean they have a religious right to accreditation by the LSUC..

There's a lot of other law that comes into play.  For example, the BC Human Rights Act allows TWU to discriminate, but the Ontario HRA specifically prohibits LSUC from discriminating on the basis of religion for purpose of participating in a profession.  Also, the legislation authorizing law societies differs from province to province -- the NS law society does not have same latitude to refuse accreditation as the LSUC does.

As for LGBT, firstly, the TWU requirement to be celibate within marriage only applies to LGBT, which is discrimination, even though it's legal in BC.  Secondly, we have minority Charter rights to protect minorities, so to argue a discriminatory policy doesn't affect many people is pointless.