The funny thing about this series is the ship potential has been pretty anemic. That's a good thing in my book, but it does make jokes about relationships a bit harder to tease out.
Honestly, she should take the AST job. Makino has always felt like a character the author didn't quite know what to do with after her initial appearance, and it's more in character for her to take a big plunge than stick around. And since AST seems to have mellowed out a bit, she's in a good position to make more positive changes in that org.