So I got the quest to trigger as normal (finally) with the bandits attacking Eisa, got the quest from her, and followed her to Moorside Inn to make sure she made it there safely. Then I went back to Frostmere Crypt and completed the quest as normal. Once I returned to Morthal though, she was gone. Does she go somewhere else after Moorside inn? Does she disappear from the game entirely once the quest is completed?

If she did disappear, I'm thinking it might be because I dead thralled one of the bandits that attacked her at the beginning of the quest.

I'm thinking she just disappeares