Weird! I have to be at work when my BF usually wakes up, & that's just because he wakes up early. I felt bad spending the night on a day he had off & waking him up early (he even drove me to work). So I stay weekends when we're both off but he will still say he wants us to spend more time together.
I wouldn't care if my BF stayed up later at all, seems very controlling.
Maybe cuddle her to sleep & do a small bit of prep for her (breakfast meal prep, getting coffee stuff ready to go... etc.) if she's feeling bad about it.
Also discuss why she's upset. It's good she's getting better but still strange that it's a problem at all.