If POTUS wants any chance of being reelected in 2012, he'll do what Clinton did and pick someone more universally respected. Emanuel was a polarizing figure from day zero, for any number of valid reasons. As the article states, when the 1994 midterms happened, Clinton bounced his Chief of Staff and replaced him with Leon Panetta, who was looked upon as much more of a conciliatory figure than McLarty was. Granted, he was still a partisan member of the White House staff (and if anyone can name another truly nonpartisan WH figure in the league of Bob Gates, I'd be VERY impressed) but he got the job done.
President Obama made a big noise during the campaign trail of bringing change to Washington, but in order to be a more effective leader in the big House, he needs to switch out Emanuel for someone who Republicans will be less likely to trash just because he's there, and will be more willing to actually do closed-door negotiations with. Basically, he should hire a moderate Democrat or even a straight-shot independent for the job. I bet his poll numbers would tick up a bit if that were to happen.