I'm just scared all the time.

[MrBond]

"It was making her miserable for me to stay."

This is what was wrong. YOU weren't making her feel miserable. SHE was making HERSELF feel miserable. It has nothing to do with you.

She might be re-evaluating her life, her goals, her decisions, whatever.

You can't control that. It's her choice to feel that way. So by understanding that, you do what YOU want to do. Believe me, she'll even start blaming you for why it rains or doesn't rain. She needs someone to blame for her feeling the way she does. Make a stand. You don't need to do it in a demanding way or being upset. Just make the decision to stand and say "WTF? this isn't what I want".