I had this happen too. I married some chick at the inn, and she immediately left the temple. I couldnt' find here at her normal spots around town, or my home in Winterrun. Then again, I didn't look too long.
Reloaded and tried another person. She dissapeared too, and wasn't in any of here spots. So I just waited 48 hours, and I found here in town. Then I told here to move in with me

I guess you just have to wait a certain amount of time.