Even if I'm doing a mass file delete, if I've got the time for it, first thing I'll do is move/rename the files to a backup / marked-for-deletion directory. Watch for strangeness. Then commit.
If it's site accounts or features, disable them, prevent them from being served, mark them inactive in the database / server. Leave them for a week or two. Then nuke.
Legally proscribed deletions (illegal content, etc.) are another matter, but most other content is eligible for a graduated approach.