It's a legitimate concern, and I can understand why it would upset some people since we're still in the middle of fighting that conflict. As the article mentioned, we're not removed from it yet as it's not become a "past" war.
That said, it's a war video game with fictional characters and events put in real-world settings. It's fiction. Plus, many games let you play as one side or the other, so why should this one be any different? It's not going to recruit people to the Taliban cause, and it's not going to belittle, disrespect or make a mockery of the real soldiers who have given their lives. This isn't going to be some joke like the JFK assassination game, or the one where you could fly a jet into the Twin Towers, so I sincerely doubt the multiplayer will have "YOU SHOT A FILTHY AMERICAN DOG! ALHAMDULILLAH!" and show pictures of dancing Arabic villagers popping up every time you frag an opponent. I also doubt the names of the soldiers in the game will be taken directly from the casualty list of the current war. As a result, I don't see how it's being disrespectful at all.
This game's multiplayer will do what scores of others have done... have virtual good guys and bad guys, let you choose a side, and then have polygons firing polygons at polygons. It doesn't really matter if it's a past scenario or a current one, it still boils down to that. And if being able to play as a Nazi, the Soviets, the Viet Cong, and other U.S. adversaries in multiplayer games has come to pass, then why not the Taliban? I don't believe there's a 20 year "wait until the war's over" clause somewhere, so...
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Strikes me as bit strange how some have no problem with a virtual us shooting a virtual them, but let it get flipped around, and then it's suddenly going too far.