Makoto always wanted a boyfriend, she never wanted to end up alone, so now she has found someone, and then in cames Nephrite, whose mere presence alone threatens to turn her whole world topsy-turvy and then they even kiss, so she's about to lose the man she's with for a man she cannot be trust because of their past. So for me, her anger works, it's understandable. It's highly unfair of course, but understandable.

Oh yay, thank God, that is exactly what I was going for! She's always wanted a stable relationship and he's threatening that without even trying, just by being himself. And she wants him, which is even worse. How dare he do this to her?