Prevent itunes from synching apps
I have many devices that sync with my Mac and carry no apps on iTunes, so it's possible. I don't back any of them up to iTunes though and use iCloud for that.
- Make a back up of your Mac/PC in case the iTunes changes need to be reversed.
- Uncheck the box in iTunes that says "install new Apps automatically".
- Choose to back the phone up to iCloud rather than to the computer
- Delete all apps from iTunes so your Library looks like this when you view apps (you can move them to trash now or leave them in the library folder as you choose)
- Test a sync of the phone to see if the apps transfer back
Going forward, purchased apps will not transfer back to iTunes from the device. Backups only back up user data and not apps - independent of whether apps themselves sync.
Once you've turned off syncing of apps for all iOS devices, you can empty the trash and rejoice that iTunes doesn't get apps unless you download them explicitly. Also, if you didn't move the apps to the trash, you can go in and delete or file them elsewhere since iTunes isn't tracking those files as part of your library now.