I was really torn by the ending, in life the right decision isn't always easy. You will always have in the back of your mind what if I'd chosen a different path? It's hard to make the "right" decision when it comes to being in a gay relationship so you make what will keep everybody satisfied by sacrificing your happiness.
In his own way I believe Kirino did what was expected of him and maybe to some degree this made him happy.
I think Kirino and Mishima became stronger because of the bond they shared even if they didn't end up together. I loved this story it was sad but very realistic like life.
Smells Like Green Spirit