Make iTunes playlist track changes in iPhone library?
Ensure you are removing the tracks from the playlist on iPhone and not deleting the actual music files from iPhone entirely. I can't tell from your description whether this is what you are doing.

Assuming you have iTunes set to only sync that playlist (or collection of playlists), by removing the tracks from the playlist on iPhone, next time you sync, the process should update the playlist in iTunes to reflect the changes made on iPhone, and remove the corresponding music files from iPhone.