Couple of things concerning Khalifa. One it's bugged at the moment, so while it's possible to save her, it's in a very convoluted way that is honestly hard to properly write out. Two, it's an alternate ending, so going back to save her will end the game and then you'll just start over at that choice and be forced into taking the normal path.
This story is honestly very linear. There are a lot of alternate early endings, but to actually keep playing there isn't much choice. That's not a complaint mind you, just how it is.