...that just means you're a rational, well-adjusted person who is not completely desensitised to violence.
That's a good thing. Run with that.
So, yeah, you're not supposed to enjoy it. You're supposed to be shocked by it and ponder its ramifications. That's a pretty bold choice for a company that could've played it safe and still raked in the dough (or even hired some lackey to do the actual raking -- because they're just that bloody rich). The problem with this sequence is not necessarily that it exists, but that Infinity Ward doesn't have the storytelling chops to justify its existence. Don't get me wrong, these guys kick ass in the gameplay department, but Bioware or Irrational Games they are not.
First off -- and it's possible that I missed something in the lead-in cutscene -- but what outcome could be worth the complicity in such a horrible act? The character you play, an American soldier who has infiltrated a terrorist network, has the opportunity to both capture/kill one of the most wanted men in the world and stop the death of hundreds of innocents. There is, for the lack of a better term, no Sophie's Choice -- no ticking bomb, no trade off to be rationalized. All I could think while playing this segment -- besides the obvious "What the hell is Infinity Ward thinking?" -- was, "Since I was the last terrorist out of the elevator, why not just shot these murdering bastards in the back and have this done with?"