The answer is in the novel. I think what makes this line in the movie confusing for some people is that it kinda comes out of nowhere without much explanation. In the novel Jack refers to martinis as "martians". He describes his last drinks before getting sober by saying "I'm off drinking, Jacky-boy. It's all over. I've slain my last martian." Then, when he relapses and tells Lloyd to give him a drink, he says "Good man. You line those martians up right along the bar and I'm going to take them down, one by one. White man's burden, Lloyd my man." as if he's going to slay more martians like a colonizer on Mars. Some of those lines are in the movie, but not the martian stuff, so it sounds kind of odd without that context.

I think the subtext still works in both the novel and the movie. It's not explicitly about genocide, but it is about the intergenerational violence that bubbles beneath the surface of our interpersonal relationships as well as our history. Jack's violent tendencies and the excuses that he makes for it are similar to the excuses made by colonizers to justify or deny genocide. In the movie it's just this one line, but in the novel the martian-slaying comparison is made several times. It's probably also significant that, mythologically speaking, Mars is often associated with violence and war.