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It somewhat depends on your situation. I recently did some cleanup and I generally got rid of as many groups as possible and moved the content to a public area (if possible). For groups that needed to stay, I made them unlisted so they didn't show up in search results.
I didn't have the problem of having users as groups owners since most groups were started by the previous community manager. If this is the case, you should tell he group owner of your shutdown plans and give them timeframe to deal with the content (with your help). 30 days is a good start. Most of the time the owner is OK with deleting it immediately and can give you advice as to where any content should go.
Much appreciated Brad!
Let the house cleaning begin.