Yeah, my wife and I had this issue with duplicates when we first got our phones and it did the "sync" to Gmail. I ended up having to go into Gmail, create a backup of all the contacts in there, then merged the duplicates that showed up in Gmail and deleted the contacts that only had emails addresses and no phone numbers. I then forced a Gmail sync to get the proper contacts down on the phone and the extras removed. Then before I loaded the backup file back into Gmail to get my contact list back to where it was I went (on the Droid Eris) into SETTINGS > DATA SYNCRONIZATION > GOOGLE, and unchecked the "Contact" sync option. Seems to have worked so far as none of my other contacts have returned to my phone after I restored my Gmail backup.
There may be an easier way to deal with the duplicates, but I didnt find it.