I'm not sure if Lee did mean to miss with his punches, but from seeing it a couple of times I do think that he was very conscious of what he was doing at times in order to minimize any actual damage he did do. At one point Lee was completely unrestrained and could have ran right into the Padres group and started to throw some punches but he ran sideways and got right behind Lou so he cold be restrained.
Matt Capps just got his suspension reduced from when he hit Prince Fielder on May 5th so Lee might not have to sit out for awhile... but knowing how suspensions work against the Cubs he'll probably be denied his appeal tomorrow.
If the Padres were smart it wouldn't even really be missing any games. Have Young appeal his suspension until he starts his next game, drop his suspension after the game, sit out 5 games and then start the next game on 1 extra days rest.