I have a suspicion that when the baby is born, Serena will struggle to bond with it as well as she thought she would and she'll realise that it's not "really her baby", and is June's. They've done a fair bit of foreshadowing of that (e.g. her relationship with her greenhouse saplings which she does see as "hers", and the situation with Janine's ill baby getting better with contact from her real mother). They're also strongly hinting that Serena could actually have children, as we know pretty much for a fact that the Commander is infertile... although, I was wondering if maybe she genuinely can't because of when she was shot?
But yes anyway, I think she pushes through the parts of it that she hates because she really believes that she'll be happy with a child... and it'll all fall apart when she realises that she's still miserable and all of the rest of it is for nothing as she's had to give up all of the other ways that she found fulfilment in life.
However... I do still think any alliance would only last for as long as it benefits her personally. She's not selfless enough to have an element of self-sacrifice.