Is this hypocritical of Obama? For the thousandth time, no, no, no. The playing field is the playing field, and once a public policy has been legally put in place you'd be a sap not to play by the same rules as everyone else. If you oppose the mortgage interest deduction as a matter of policy, you still have every right to take the deduction as long as the rest of the country keeps it in place. If you're a Republican governor who objects to the stimulus bill, you'd be actively irresponsible not to take your share of the money once it's there. If you oppose earmarks, you still have an obligation to your district to take them as long as they exist.
In order for the President to be in any position to do anything about Citizens United through legislation, he still has to be President. That means playing the campaign finance game that SCOTUS has set up so he can get re-elected. The alternative is a Republican in the White House who would certainly veto any campaign finance limitation, not to mention have the ability to appoint SCOTUS justices...and three of them are currently in their 80's or will be in 2013.
David Axelrod signals the White House stance:
We have to live in a world as it is, not how we want it to be.
You can hate the game, but you still have to play it. And you play it to win. Period.