First off, I am an active duty Air Force member.
It seems that this whole thing is being misinterpreted by the community based upon a possible misunderstanding of how the Army and Air Force Exchange Service works. Hopefully I can illuminate the situation. It is a series of retail outlets that serves ONLY military personnel. If you aren't in uniform, they will ask for an ID card for every single purchase. This is largely due to a lack of sales tax and other savings. AAFES is supposed to exist as a benefit in return for our service. These stores are not comparable to Wal-Mart or Best Buy even though they look similar. The whole thing is run by the military, even the few on base GameStop's operate as vendors with the permission of the military.

Why did AAFES decide not to stock Medal of Honor? Out of respect and sensitivity, as mentioned by Major General Casella. This is not about violence, censorship, political correctness, Jingoism, morality, or anything else. If you walk around a BX or a PX, you will only see three types of people: active military members, retirees, or immediate family members of servicemen. That means that the number of people affected by the war in Afghanistan is astronomically higher than in a civilian store. Those are the people who WILL be affected by a death in Afghanistan. A real world game might be too much to handle. Do you really want to see a little kid show the game to his mom and ask if that's where daddy is? Absolutely not, but it could happen. Picking up Call of Duty: Black Ops? Completely different.
The difference between this game and other military shooters is that it is real and it is current. Fictional games are really no different than a summer blockbuster, and games set in real conflicts have always had at least a generation of buffer space between participants and audience. I wholeheartedly believe that Danger Close went to great lengths to make the singleplayer respectful. I appreciate the effort. The problem is that multiplayer can't have that redeeming effect that story provides. It's just a name change from CoD's "OpFor" to Taliban, but that can be enough.
Keep in mind that this decision only affects military personnel. If someone buys this game on a base and gets upset, they are probably entitled to be. More than likely, they've been there or have been affected by operations there. Is anyone really going to tell a recently returned troop that they are being overly sensitive because they get upset watching Americans play as the Taliban killing other Americans? By not stocking the game on base it becomes a personal decision to buy it and keeps it out of the spotlight. AAFES doesn't have to worry about impulse buys or scenes from veterans or complaints. They are choosing not to endorse something that might upset their clientele. Military life is stressful enough, they are merely trying to be sensitive to the pain of their patrons. It would be in poor taste to advertise a game where the player can kill Americans as the Taliban to an American who might be killed by the Taliban in the near future.
If we want to buy the game, going off base isn't really an inconvenience. We aren't confined to base, so access to the game is in no way being denied (maybe in really remote locations). Most military gamers will probably still pick up the game and won't have a problem with it. The gameplay mechanics won't be any different than other recent shooters, but the locations might be more familiar. Probably not a big deal to most. But again, this isn't about most gamers. This is about people with PTSD or anxiety over a deployed loved one or some other painful trauma. The BX is one of the first and last stops when returning from and leaving for a deployment. A soldier who returns from firefights in Helmand province should expect painful or insensitive reminders off base in the real world. But shouldn't they be spared while on base?
Are the people playing as the Taliban playing any differently than in Modern Warfare? No. But it's about the perceptions of that minority who fight the wars the rest of us turn into entertainment. What it comes down to is that AAFES doesn't care what servicemembers buy, they just try to provide whatever it is that they want. This particular product won't do a very good job of satisfying the customer if they find it offensive or disrespectful. In a normal retail outlet, publicly banning something under those circumstances would be unacceptable. Luckily, this isn't normal.
As for me personally, I had already preordered the game from Amazon. I don't have any problem with the content, but I certainly won't show it around base. I actually deal with Operation Enduring Freedom everyday and expect to be deployed to Afghanistan within a year. I want to go. Anyways, sorry for the diatribe. I felt I could offer a rational military perspective on the issue. Please consider some sort of feature on reactions from warfighters. This is one of the only real videogame news outlets that can run in depth opinion pieces. For an issue like this, a comments section probably isn't enough.

Ed's note: Please take a moment to read another take on the issue from a former Army Medic.

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