Best thing to do is never sync with iTunes. Just detach completely.
I set my iPad up (and my new iPhone) without iTunes at all. iCloud backup let me move from an iPhone 4 to 5 without a USB cable at all and all my data moved over perfectly.
I plug in to my computer to transfer videos that don't transfer using Photostream. I also occasionally will do a sync of movies for a trip.
Music is iTunes Match. Photos are Photostream. Email is IMAP. Contacts/Calendars/etc is iCloud.
It actually works very well and I'm able to move to new devices or restore from a backup without issues.
