Pretty sure Apple knows this is an issue by now but just won't do anything about it--or don't know how.
I have had a program called CopyTrans for years now, and I just use the CopyTrans Manager program when I have issues like this. I delete the duplicate playlists off iTunes, then connect my iPhone to the computer, open CopyTrans Manager and delete the duplicates off the phone that way, "update" in CopyTrans Manager and then it's done.
BTW, when I just had this issue this weekend, I directly modified the playlists in iTunes on the computer, not on my iPhone, and I still ended up with duplicates. I'm seriously considering just 100% using CopyTrans to manager my iPhone.