I would have guessed that he never saw Midna as a serious threat, so he didn't really have a reason to kill her. After all, Midna's plan relies on collecting an the fragments of an ancient mask to take on Zant, whom is much weaker than Ganondorf as we know. Once he broke it her plan was stopped and she was reduced to being of little threat to Ganondorf while she was in her current form.
HOLY CRAP!!!!!!!! but maybe that's because she's the Princess of Twilight. maybe he CAN'T kill her. I don't know
I think it would have been quite easy for Ganondorf to kill Midna if he wanted to. Zant nearly does so when he uses the Spirit of Lanayru to weaken her, and he has a fraction of the power that Ganondorf does.
So I would personally say that there isn't a chance for Midna to be backstabbing Link, particularly since she's never actually achieves anything in that works in favour of Ganondorf, she only actually helps to remove the parts of his kingdom that he has used Zant to take over.