Yes they would retain organizational control. But with the Democratic Party having lost 2 seats because they ate their own favorite sons via the primary system, it is no assurance that the Democrats - even if they got 49 seats - could assure that the 2 independents would hand them control. The party failed these 2 Senators, letting the fringes take control of the primaries, only to lose the general election to the people the party should have supported.
What I am saying is not only is that party a mess, there is no assurance that the two independents wouldn't want to deliver some payback.
I don't see Lieberman as being anything other than he has been in the Senate up until now; he will vote with the 'Rats the large majority of the time, but might support the Bush administration occasionally on foreign policy matters. In other words, no discernable revenge factor. He'll count his blessings to be reelected and move on as if almost nothing happened.