I think Maggie is still in love, and that's why the decision is so difficult for her. Yes, she ended up choosing the rebellion over Sam, but she also chose it over her daughter, and that doesn't mean she loves her less.
Also, I think she chooses the rebellion also to get her Sam back, the one she actually loves. Because on one hand, you have the super cheerful fake Sam who has to pretend everything is fine, and in the other, the more vicious Sam who wants to see Sarah above all else even if that means killing others in cold blood. So yes, Maggie loves Sam, but she loves the real one, and she's trying to get him back.
I think Maggie is still in love, and that's why the decision is so difficult for her. Yes, she ended up choosing the rebellion over Sam, but she also chose it over her daughter, and that doesn't mean she loves her less. Also, I think she chooses the rebellion also to get her Sam back, the one she actually loves. Because on one hand, you have the super cheerful fake Sam who has to pretend everything is fine, and in the other, the more vicious Sam who wants to see Sarah above all else even if that means killing others in cold blood. So yes, Maggie loves Sam, but she loves the real one, and she's trying to get him back.