I can't think of a single work with an anti-war message that doesn't have guns in one form or another. You can't really show their devastating effects without them being in it, I suppose. MGS tends to reward you more for not taking a life as opposed to killing, at least since MGS2, so it's ironic that a game that has grown over the years to have such a dim view on violence actually funds companies that create instruments that can be used to perpetrate such violence.
I guess I am one of "those" gun-control proponents, although I'd say I'm more anti-bullets (XD) If I'm honest, I do like guns (and indeed violence) in a fantastical, cathartic and even fetishistic sense, but I'm not too keen on the idea that my fantasies (so to speak) pay towards funding instruments that can be used to commit real-life violence, if that makes sense?
Cars aren't designed to kill, so that's not really a fair comparison... and let's not talk about "realism" in Metal Gear.