I think the implied intent of the player character counts for a lot when it comes to colonialist vibes. "Oops, I didn't mean to be here, and my main goal is to leave" is a step away from any sort of colonial undertaking.
As for accepting it, I'd imagine it's because the game doesn't really give you a choice. There isn't a way to coexist with the native species -- they're always aggressive even if you don't create pollution (they're just not drawn to you without pollution; they'll always attack if they see you). In your metaphor, it'd be like if we never did anything but shoot at the alien. So you can either just not play the game at all, or you can exist in conflict with the native species.
It'd make it a very different game, but it'd be interesting to imagine there being some way to work with the native species. If you could make the choice between a quick and dirty pollution-heavy resource-extraction "bad path" and a more complex social cooperation "good path", that'd probably trigger you feeling guiltier about casual extermination.
As for accepting it, I'd imagine it's because the game doesn't really give you a choice. There isn't a way to coexist with the native species -- they're always aggressive even if you don't create pollution (they're just not drawn to you without pollution; they'll always attack if they see you). In your metaphor, it'd be like if we never did anything but shoot at the alien. So you can either just not play the game at all, or you can exist in conflict with the native species.
It'd make it a very different game, but it'd be interesting to imagine there being some way to work with the native species. If you could make the choice between a quick and dirty pollution-heavy resource-extraction "bad path" and a more complex social cooperation "good path", that'd probably trigger you feeling guiltier about casual extermination.