I'm in the same boat. I became vegan a few years ago for purely health reasons. Now in the last couple of months I'm starting to become more of a morally conscious vegetarian and think that the way factory farmed meat is slaughtered is just wrong. But there's where I stop. I still question the moral difference between killing plants or microscopic organisms and that of organisms in the animal kingdom. So basically if you kill and prepare the animal yourself that's fine, just so long as its done in a way to minimize suffering.