(and here's me in a new fandom. like whoa. no ownage, no insult intended. did not turn out the way i imagined it, but at least it turned out at all.)
They all have theories.
Sophie thinks it's some sort of deep seated emotional trauma, originating in childhood. She's got dozens of scenarios in her head, each one bloodier than the last; hunting accident, convenience store robbery gone bad, whoring mother caught at it by alcoholic father. All the romantic clichés, really. Her favourite is the one where he finds his Daddy's loaded gun hidden in the closet, drops it, and accidentally kills his sweet, golden haired little sister.
Hardison thinks it's because Eliot is a technophobe still stuck in the Dark Ages, who would knock down Progress with a blunt instrument if he ever met it. Sometimes Alec looks at him, shakes his head and mutters something about cavemen and astronauts, and Eliot lets him think he doesn't get the reference.
Parker thinks he's afraid of loud noises, like a dog with fireworks, and Nate...Nate thinks it's because of that thing in Croatia.
They all have theories, and they're all dead wrong. Not that he's going to tell them that.
Eliot likes theories, likes to be the man of mystery. Likes that the only real thing most people know about him is that he always gets the job done. Likes to be underestimated; hell, likes to be overestimated, he can work with either one. He knows how to use the power of rumours.
It's not like the truth is embarrassing or anything. And it's fairly obvious, too, just not what most people expect from muscle. So?
One reason is pride. Guns lack...artistry. Anyone can kill with a gun. It's cheap, and in some deep part of him he feels using guns is cheating, that it shouldn't be so easy, taking someone's life. It could be argued that he's a hypocrite, since taking lives is pretty damn easy for him too, when he wants to. Could be argued that he's a cat complaining that the mice are calling Acme for a box of dynamite. But it wasn't always easy, was it? He's worked hard for it, works hard still, and mice can bite hard when they're cornered. There's no need for any TNT.
He doesn't believe in fair play, not exactly. The world doesn't work like that, he doesn't work like that; but he believes there should always be a chance of succeeding against the odds, no matter how small. If there were no million to one chances, he'd have been dead long ago.
Eliot does believe in balance. He knows that every so often, someone will come along who is better than him, or maybe just luckier, and then he'll need that miniscule chance. You reap what you sow. His Momma told him that. And maybe she didn't mean it quite the way he means it, but it's been helpful either way.
The other reason is, you can dodge a bullet. You can duck. You can throw something else, someone else, in the line of fire. Eliot's done all of them, many times. You can be shot. He's done that, too. What you can't do, with a bullet, is fight. Oh, the man with the gun, you can fight him, but you can't fight the bullet.
If you can't fight, there's really no chance at all. And that's why he hates guns.