So let me try to understand what you want to accomplish.
You have synced your iphone with iphoto via itunes. You see the same thing in your photos app as you see on iphoto on your mac and you want to remove the pictures from your iphone and keep then in iphoto, correct?
If this is so you need to go itunes, click on your iphone under devices (left hand side) go to photos and then under the drop down menu "automatically sync" select "no events" and then make the selections below that you want to sync. This will remove anything you don't select and keep anything you select. I would make sure your iphoto library is current and synced by following the instructions here http://support.apple.com/kb/HT4083?viewlocale=en_US&locale=en_US.
Let me know if I misunderstood your question.