Besides Ninkovich and Hendrickson, Malcolm Jenkins immediately comes to mind. Payton himself said it was a huge mistake to let Jenkins go.
If you're not referring to just defensive players, there was also TE Cameron Brate. He may not have been all-pro, but he was really good.
Every NFL coach has let some players go that have gone on to do well somewhere else. Some coaches have done it more than other coaches, but they've all done it.