If you haven't yet, I'd highly recommend reading some of Temple Grandin's books. She's designed the system used in nearly all US slaughterhouses, citing her autism as a way to help her understand how an animal might feel going through one, thus making the process more humane. She's had to come to terms with similar issues and her passion is constantly questioned by people who ask her how she could be responsible for the slaughter of millions of animals yet still say she loves them. The short answer is that realistically, most people will eat meat and factory farming will continue, so it's better to improve the process so the animals involved can experience better welfare. She's also said that nature is cruel and many animals die long, painful deaths everyday, so to be a food animal that's treated humanely and given as quick and painless a death as possible isn't necessarily the worst thing in the world. I'm not sure if you've ever seen the slaughter process, but it certainly doesn't seem like a terrible way to go. I know it can be hard to put your emotions aside, but if you look at it as though you're promoting the industry, you'll make it harder on yourself. I think it's much better to work to improve the health and welfare of food animals rather than turn your back and allow unnecessary suffering to continue, even if you don't agree with the process.
Anyway, that's just my two cents and Temple Grandin says it much more eloquently than I can, so read her books. If this is an issue you're really struggling with, her perspective might help you.
I'm a vegetarian by the way.