What you propose IS treating religion differently under the law. The Church, having bought its space, has free speech rights, just like everyone else. The school's policy is blatantly unconstitutional.
If that's so, then prohibiting beer ads, tobacco ads, political ads, ads for NAMBLA, ads for the local head shop, ad nauseatum, is also unconstitutional. What's being challenged here is the authority of school officials to decide what is or isn't appropriate to post on public school property.
Frankly, I think this is something of a straw man argument, because a more fundamental issue is whether or not the school should be selling ad space at all. If it's okay to do what the school is doing, then selling wall space for cigarette ads to raise money for lab equipment is no different.
Should public buildings be used as billboards? I think not. For one thing, issues like this one would be moot. For another, the idea of the word "PEPSI" painted down the length of the Washington Monument is somewhat distasteful to me, for some reason.