I swear to God, once she left the church in Riften I haven't found here anywhere anymore...

If it helps: I have all the houses available in the game (including heartfire houses).

Wait, what? You got married in a CHURCH?!? I got married in the Temple of Mara...

Jokes aside, your best shot is to reload a save and make sure you talk to her BEFORE she leaves the temple. She should have gone to Jorrvaskr, but since she will walk there, it
might take her a couple of days - there are reports of spouses gone missing though (unless it's been patched, but somehow I doubt it).