I had the same situation with Miranda being angry because I went with Jack. She stayed like that for the rest of the game. Knowing she was not happy with me, I didn't assign her to any roles during the suicide mission. I didn't want to risk her making a mistake and getting herself or any other member killed. Miraculously, everyone managed to survive.
People are disappointed with ME3's ending because there was no suicide mission equivalent. Where the choices you've made through out the game have a consequence in the end. ME2 would have had a boring ending if your only consequential decision was to either destroy the collector base of not. Which is what ME3 ended up being like.