I'll put things simply.
People are focusing on the violence itself, but miss the entire point of the context. That violence in terms of "being like what we see on the news" is part of the story and also exists to raise very specific questions.
As I pointed out in another thread on the subject, the point that is being made here is "Would you sacrifice a bunch of innocent civilians, to potentially save millions of lives?". This is like a James Bond movie minus the camp. We're basically dealing with the hypothetical "Liscence to kill" super agent that is the weapon of last resort, and here he is employing that lisence to kill.
The scene does not cut any corners about what is being done in that situation, but in the end the correct answer is "yes, I would sacrifice the innocent people". There really is no other answer given what the costs could be if this was not done.
While I will agree that showing things this graphic to children is wrong (it's "M" rated for a reason) we do not live in a perfect world, and arguably I feel children should have points of view like this explained to them early on as they grow up. Kids raised with an optimistic "there is always a perfectly clean and acceptable solution" are likely to have problems later when confronted with reality.
I think one of the problems with say 9/11 for example was the fact that it caused many in our country to lose their innocence. The way many were raised, something like that should not have even been possible in the real world. A lot of our current politics now just short of a decade later revolve specifically around the system shock that gave us, with a lot of people fighting against the reality check as much as they can.
I think that Modern Warfare 2 is contreversial in that scene because on a lot of levels it shows the world as it is. A really gray and messed up place... compared to the purely "Black and White" domain of most shooters with clear cut good and evil, where the worst you can usually say is that the protaganist you play is ruthless (albeit usually with good reason). MW2 isn't just "ruthless" there is nothing 'good' about that situation unless you approach in in a "big picture" kind of way and even then it's quite disturbing that such a thing should ever be nessicary.
As far as the early hype about horror comics, well that's exactly what video games are facing. To be honest the earlier generation always calls the new media "too powerful" and oftentimes don't like the way the world changes from how it was when they were young. The new stuff is always an exception.
Honestly I think we're dealing with irritated baby boomers who went against their parents more conservative beliefs, only to find they were right about a lot of things. Just as their parents complained about their music, comics, modes of dress, and beliefs, and were out of touch with a lot of what was happening in the world, the boomers are now facing the same thing themselves. Where they had their dreams of peace, love, doves, and flowers, we now have to deal with a very gray and nasty world that is no longer at peace. Their entertainment was "too intense" as their parents put it, well now media has improved again and they are basically their parents.