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Its the main temple one would go to when they wish to pray to the Twelve for guidance. Its kind of like a Mecca of sorts. I doubt it will serve much of a purpose at all until 3.0 or later but if you look at where the Scions pray to the Twelve to summon the prison of light in "End of an Era" it looks like Thancred was praying there.
Not exactly! The Sanctum of the Twelve is simply (from what I understand), a cathedral built in honor of the Twelve from a very long time ago, only recently found in the Shroud after the Calamity. The NPCs there are currently trying to renovate it so that we can access it in future patches; the devs mentioned a while ago that the main purpose of it is for character marriage later on.