You can delete handles. You just have to go through each layer one by one to find them all. (There is a column in rigging panel with a count of the number of handles in that layer, so this is not *that* hard to do.) I would go this way if I want to keep triggers and swapsets etc. To delete, you single click on handle so marker turns white then hit the DEL key to delete it.
You can reimport artwork and start from scratch. You will have to do any behaviors and behavior properties again, and triggers. But it would be a freshly clean puppet. I do this if I fear the puppet got corrupted. More work, but more confidence the puppet is not the cause of my problems.