I think we have to accept it as a fact that Othello truly loves Desdemona even though he kills her. That is the essence of the play, the essence of the tragedy--that a man kills the woman he loves more than anything else in the world. During the scene in which he kills his wife, we can see that he is emotionally torn to pieces. He is doing something he doesn't want to do. If he didn't love Desdemona it wouldn't be hard for him to kill her. He should have had a better motive. He allowed himself to be made a fool of by Iago and that business with the handkerchief. This may make it seem that he didn't love Desdemona enough to give her a chance to exonerate herself. I think the best speech in that scene is the one in which he says to Emilia:
Had she been true,
If heaven would make me such another world
Of one entire and perfect chrysolite,
I'd not have sold her for it.