Then I spend the next half hour looking at the connected device to ensure my collection is still there.
It's part of the reason why I switched over to the (defunct) Rdio. Managing the individual iTunes music files was just too stressful.
You could 'chflag -R schg' the entire music dir, thus making it immutable - even for root - without chflagging it back.
Then there's no more syncing risk. Just saying.
Sync is one-way - what could you lose?
It's far safer to plug your phone into a Windows machine and using the file system GUI to copy the photos to the folder you want. Using Preview to import the photos as if the iPhone is a scanner is another safe method.
The multiple user/multiple computer problem that you're referencing can probably be solved by logging in to the corresponding icloud account on the computer.
And if you don't want to trust iCloud with photo sync, there are other options (Dropbox does that, and Plex has a photo sync function if you want to host those files yourself).
To add insult to injury it's almost impossible to make a file-for-file backup before decimating a device with iTunes sync. In fact, the iTunes sync process is the main reason I stick to Android despite it having a whole other ecosystem of flaws. I'll take a USB Mass storage device and robocopy / rsync, thanks. They actually work.