Steps to delete unwanted email ids from the phone when all contacts- phone no. and email ids are synced between Gmail and phone)
1. Export all contacts from Gmail to a google csv format file
2. Delete all contacts from Gmail except the ones you want on the phone (was easy in my case as i had a separate group where i stored my phone contacts)
3. Delete all contacts on your phone (Make sure you set to display every contact under display contacts options)
4. Sync Gmail and phone
5. Once sync is completed switch off the sync feature and never activate it again
6. Import the google csv file back to Gmail
Thus your Gmail will have all the contacts that it had before and your phone will have only the ones you wished to retain.