"Fitz and Simmons’ relationship takes a blow. . ." yes, but, they're transitioning from "giddy lab partners" oblivious of each others attraction, into an adult relationship. A bumpy road, but likely a better destination.
And I question the "A.I.M" (had to look them up, had never heard of them.) Glad to have confirmed…

And as Coulson pointed out, she was also allowing herself to be captured/imprisoned, in exchange for saving everyone. It showed she had her priorities right.