I don't think that staying in europe would do harm for them in the league specially this season. Last season was another story, they didn't have the depth that they currently have. Today they've played with 8 different players than the once that usually play in serie A. Only gattuso, kaladze and Jankulovski were the regular starters !! And in the last 15 minutes ronaldinho came in and scored.
Win or draw tonight, they'd have certainly qualified for the next stage, that's why i don't really care about their win tonight.
The thing is, if Milan stay longer in UEFA Cup, they will want to win it and in order to do so Ancelotti will start using his best players when they'll be up against more tough opposition. And we've seen how things ended when Milan were going after 2 trophies (CL and scudetto) in 2005 and 2006. They left empty-handed.
On the other hand, when they concentrate on one single competition, they usually end up winning it.