Instead of making them go away altogether can't you just have somebody moderate the groups, and oversee things, and delete groups that have been inactive for so-so amount of time?
And can't there be a process where instead of letting people just up and make new groups and have it go through, make it go through some sort of an approval process before the group gets created?
It seems sort of crappy to get rid of groups for those who actually have active groups.
What? The groups aren't going away because of people's behaviors in them. Read the posts from Cheapy for an explanation as to why. It is purely technical issues with the site upgrade.