I think the "They made their choice" was more of like a "we don't have time to argue, Madi, we need to go now." And also just that, honestly... she cares more about Madi than she does about Bellamy in that moment. Which is fine to me. :shrugs:
Bellamy did choose to betray her. From her perspective, all he gives a heck about anymore is Spacekru, she doesn't know he poisoned Octavia for her. And before anyone says "okay but Clarke wanted to take out O..." She literally before she got arrested recognized and explained to Bellamy that she regretted the idea.
I do agree that if they forgive each other by the finale, it is very rushed, though. I do wish that they had more episodes in the season to forgive each other.