It was a bizarre cover, as I can't see why it's relevant to anything in the magazine, but for the campaign to get so uppity about it... well, surely they knew this was going to happen? Because of their overreaction, almost everyone wants to talk about it, comment on it, satirise it, satirise them, and so on.
If Obama's people can't take this sort of thing when he's not president, imagine how things are going to be if he wins? George H.W. Bush, Bill Clinton and especially George W. Bush have received more than their share of abuse in the form of mockery by the talking heads all over the globe (I mean, come on, there's an entire industry based around taking the piss out of George W.). If Obama's people can't learn to let things slide off them, like water off a duck's back, then they're in for a really miserable time in Washington.
If I really think about it, I was surprised to see the cover, but I've seen much worse about George W Bush and Clinton, that really I couldn't bring myself to care or even do a double-take. It was only after the fracas began that I decided to get a copy of the magazine and see what all the fuss was about. (This, I bet, was the case for a lot of people - sales of this issue will probably be more than their usual.)
I don't think anyone wins in this sort of situation, expect editorial cartoonists, Jon Stewart and Stephen Colbert (I have no idea if the latter two have commented on the cover, as it now seems to be impossible to get The Daily Show or Colbert Report on the internet while in the UK).
Perhaps not the smartest editorial decision, but come on people, there are far more important things to be discussing or getting angry about. Let's move on.