You certainly can sync your iPhone with iTunes without having anything associated with your MobileMe account disrupted or changed on your iPhone.
I have a MobileMe account accessed with my iPhone and iPad syncing contacts, calendar events, Safari bookmarks, and notes over the air with both devices along with syncing both devices with iTunes for transferring music, movies, tv shows, podcasts, 3rd party apps, and photos from my computer. Nothing is disrupted with my contacts, calendar events, Safari bookmarks, and notes with either device when transferring the other data via the iTunes sync process.
Simply don't have anything selected for syncing under the Info tab for your iPhone sync preferences with iTunes. Syncing with iTunes is the only way to remove photos on your iPhone that were transferred from your computer via the iTunes sync/transfer process.