I'll be honest, I haven't read the whole thread up to this point, but I wanted to make a couple of points that didn't seem like they'd been made already:
(1) Whether we do, in fact, eat a lot of meat has no bearing at all on whether we ought to feel guilty about it. Similarly with arguments about whether we are 'naturally' disposed to eating meat - the fact that something is natural, or generally or universally the case, can never be used to determine whether it is a morally good or bad thing. Same with the 'the animals have been bred for slaughter' line - what they are in no way determines, by itself, the way they should be treated. Finally the variant that says 'other animals eat meat, no problem there!' True, but we don't think that animals are morally responsible for much, so why should we bring them into this? Animals do an awful lot of things I wouldn't. Philosophy students will be familiar with the idiom 'an is doesn't imply an ought' - it's called the Naturalistic Fallacy and it's never going away.
(2) Another irrelevance is the health issue. We don't have to eat meat - maybe we can also be healthy without eating vegetables but again that's irrelevant. We can be perfectly healthy as herbivores, omnnivores or carnivores so no option involves an imperative to our own survival or flourishing. Breathing, we ought to do, because if we don't we'll die. Meat? No obligation either way.
(3) Since it only makes sense to feel guilty if you think you've done something wrong I take it that whether you ought to feel guilty hinges on whether eating meat is morally permissible or not. The only valid arguments I can see in favour of eating meat are the following:
(a) Animals are not morally relevant (or some fact about animals makes them morally irrelevant).
Animals don't suffer in the right way, don't think like we do, aren't intelligent, aren't a part of the moral world etc. These arguments are, I think, pretty much the only ones that work. Except that they involve some pretty unpleasant commitments. Say, for instance, that eating meat was acceptable because animals are of inferior intelligence. If that was true then you would have to be prepared to admit that it was also acceptable to eat (and farm!) humans with comparably inferior intelligence. The same argument applies across the board with (a) type examples, and I really don't find the result that appealing.
(b) The amount of pleasure to be had from eating meat outweighs the suffering of the animals involved.
So, arguments of the form 'animals don't suffer much when they die', or '(certain) animals don't feel pain like we do'. As regards the first, I don't think it works simply because the act of killing and eating an animal denies that animal a future life. You're not just giving it a moment's pain while it dies, but you're denying it the possibility of the pleasure of its next so many hundred meals, mates, whatever. If their pleasure feels anything like ours, or valuable like ours is, then there's no way that the tastiness of a meal outweighs the tastiness of a hundred.
(b*) An interesting variant of this is "if we didn't eat them, they'd all die anyway". I see what it's trying to do, but us getting at least some pleasure from what will in any case be a horrible situation (having to let the vast majority of our livestock die) really doesn't work as an argument. When bad shit happens we do not think it's appropriate to find pleasure in it, especially if that leads to more of it happening!
(c) My freedom to eat meat outweighs the suffering of the animals involved.
Freedom is important, so we might think that banning meat would be an intolerable intrusion, but we know that freedom to do something doesn't mean there might not be a very good reason why you shouldn't. I'm free to sit at home all day arguing on the internet, for instance...
So, should you feel guilty? That's a pretty interesting question. My instinct would be to say yes - if you eat meat, and eating meat is a moral transgression, then guilt is appropriate. For the reasons above, I just don't think there are any good arguments against the position that eating meat is immoral. Maybe you think there aren't any good arguments in favour of vegetarianism either, but then I ask you why take the chance? If you thought there was a pretty even chance that what you were doing was immoral, and it was so easy to not do it, would you risk it? That's pretty much your choice.
Another interesting question is whether those who don't feel guilty are doing something wrong. Here I think it's more debatable. I don't think there can be anything wrong with not feeling guilt, even when it is appropriate, just because feeling guilty isn't a voluntary action. There might, however, be something wrong with not being the kind of person who felt appropriate guilt, if you were capable of changing that.
Tl;Dr - Most arguments in favour of eating meat are either false or fallacious.