No, she didn’t understand him. Literally five seconds before that, she was reading Zuko’s letter and he was trying to explain 1) why he left, 2) why he couldn’t drag her into it, and 3) why he thought his country needed him to do this. He literally said “Stop. This isn’t about you. This is about the Fire Nation!” and Mai says “Thanks, Zuko. That makes me feel all better,” and threw the letter at his head. Zuko then tried to elaborate by saying he was saving his country, and that he didn’t see his actions as a betrayal to her or the Fire Nation.
So, no, she didn’t understand his motivations at all when it came to that final cut-away with Zuko and Mai locking eyes. She didn’t even respect his motivations and decisions. Her rescue of Zuko made the least sense out of anything from that episode and the lack of explanation/development for that moment was glossed over with “I love Zuko more than I fear you.”
Well, Mai… you can say that all you want, but your actions until that point speak differently.