"Good men don't need rules. And today is not the day you want to find out why I have so many."
This quote really rings a bell with me, and is a big part of why I love the Doctor. He's a great big extended "with great power comes great responsibility" metaphor. As long as the angst doesn't reach critical levels (and, granted, it arguably has several times) I like a little second guessing in my timey wimey heroics. It keeps him grounded, and stops him from going all psycho lord of time again.
I wouldn't call this a win for magic. The whole time, Batman is trying to blast Equinox away with magic and, in the end, it fails. What really won the day was logic, in the finest tradition of Captain Kirk arguing a computer to death. #batmanthebraveandthebold