It should, of course, but games typically make humans Bad Guys that are trying to do Bad Things, so shooting them is given some moral justification. Most players wouldn't feel comfortable about a game where you're tasked with blasting a bunch of unarmed orphans, for instance, even if the gameplay is exactly the same. That's why the content of this title feels like poor taste.
I've never played the title, so you'd have to be more specific. But it's one thing to use a scene of slaughtering innocent people for dramatic effect so as to make the player purposefully uncomfortable, and another thing to do so by accident. The tone and context matter, I think.
Each side being on some sort of equal footing does make a difference. If one side always had rocket launchers and the other side had no way to fight back, I don't think players would feel quite the same way about how the matches would play out (besides being a pretty crappy game). Even though the games are just as fake and nobody's actually getting killed, there's little satisfaction in gunning down a bunch of fake things we don't feel are deserving of it.
If the game were populated mostly by lions, tigers and bears (oh my!) that'll eat you if you fail, it wouldn't be quite so offensive as gunning down a bunch of meerkats. It's kill-or-be-killed mentality at work. But developers could make the same gameplay even less offensive by justifying it with some backstory ("You're stuck in the wilderness and must escape deadly animals in order to reach civilization!"). These framing devices matter because of how they set the tone.
