If you had a search engine, would you list sites that had ceased to exist?
It isn't a penalty, it's a no brainer. You'd remove them, and restore them if / when they returned. And if they did it again, you'd probably be slower to reinstate, in case it got to be a habit.
Don't forget Quadrille's Oft-Quoted Tenth Law:
Search Engines are not a service for webmasters - when you assume that they are, you see penalties when they are just doing their job.