Not really, no. Where do you see religious tolerance in the game? Priests can easily call on mobs to go and kill believers of other religions, for example. How does that amount to religious tolerance?
Existence of something does not mean the nonexistence of its opposite. Can priests "easily can on mobs to go and kill believers of other [evil] religions"? Yes, they can. But they very seldom do. And doing so causes a bunch of people to lose faith. In my eyes, all of the faithful lost were tolerant people that wanted nothing to do with persecution of others. And all of the priests who chose not to use this option make a show of tolerance. And even faiths who consider some others evil rarely give that stance to more than one or two other religions.
If you insist that there should be a way for having multiple temples of multiple religions in the same regions, then having them built by priests instead of lords would be the proper solution. That's a solution that makes sense and can be discussed, but it does have consequences that you should think about as well.
The most commonly proposed solution, I believe (or at least the what appears to be the best compromise to me), would be for the priest to be able to propose building a temple to the lord, by clicking a certain link, and then having the lord being able to click a link he'd receive to accept.
