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From what I understand Obama merely said that he wanted Lieberman to caucus with the Democrats. He never expressed his opinion on whether or not he should keep his chairmanship. And you have to think of the alternative - could Lieberman do more or less good on the other side of the aisle? Which would be the worst scenario for the Democrats? If the worst scenario is having him bolt, then they would probably want to look out for their own self-interest, which, yes, appears wimpish, but is likely better than the alternative.
Also, I read yesterday that Lieberman has a disapproval rating of over 60% in his home state of Connecticut. If this man gets re-elected once again, then I think the problem lies with his constituents, not in the Senate!