I think both had their own reasons to do what they did with Penny, and both were right in a sense. The Gov was keeping her because she was the only thing he had left in the world, the only family he had. To him, she wasn't dead. She was just very very sick (probably the reason he had Milton doing all those experiments). He wasn't keeping her around for malicious reasons. True, he is a bad dude in several other areas, but in regards to Penny, it's not much different than the Hershel situation last season (except of course, he's feeding her people). And of course, that makes Michonne his Shane.
But then, from Michonne's perspective, this girl isn't sick. She's dead. While she was putting the girl out of her misery, I think a big part of why she did it was to stick it to the Governor. To push him, so he could push back.
t:.
