Set my phone contacts to sync to Google not Google to phone
When you're done organizing your contacts on the Google Contacts page, and before syncing with your phone, go to Applications->Manage Applications and clear data+cache of the contacts app (plus some other service I cannot recall currently, something like a contacts provider if there is). Then open your contacts app to verify no contact is left.

That done, sync again -- as there are no contacts on your device, it cannot upload anything (and thus not mess things up again), but should simply download the data from the Google server.