I think the biggest issue is more of one of practicality and exposure than anything else.
The issue with many of the arguments, including the freedom of religion, though well thought out and I do appreciate the thought, is simply this:
There has not been a real religion in the Empire, Diamond Dogs, or even Crystal Empire since the fall. And there has not been need of one, nor has magic been a real issue. Pretty much all religions, if any, are small and very much so depending on the region. A point of fact would be the Ancestral worship practiced by the Griffons, or maybe the Religion of Love in the Crystal Empire. Plus, well- an Empire the size of Griffonnia is too large to have so many disparate cultures and religions, if any, so close to each other. And one religion overall never really works. The interlude should probably involve a lot of, well, arguing. Too much diversity, ironically, leads to a lot of arguing. It's a tough one, I will tell you that.
That being said.
I do believe that the Council of Nicaea should be less what religion we should take, or if we should have a piety option and more about diversity, in that the religions should have a conclave, and multiple opinions and options. A Dynasty of Drunkenness, by torroar, has the Piety options as, well, an inclusive option. Building temples to more, Sigmar, Ulric, Shallya, and such.
Sorry, too much rambling