The point of "syncing" in iTunes is to force-download items (songs, photos, etc.) from a computer to an iPhone or like device. Each "sync" ensures that the iPhone contains the set of (songs, photos, etc.) selected on that sync is on the phone, and any items previously synced but no longer selected are removed. The latter is how you removed iTunes-synced items from the device: re-sync with those items no longer selected. In the extreme, re-sync with no photos selected (e.g. by selecting only an empty folder) to remove all previously synced photos.
As you learned, enabling iCloud Photo Library also removes all iTunes-synced photos, since Apple has declared the two syncing mechanisms mutually exclusive.