Just as a review: In iTunes, you are going to Edit > Preferences > Devices, the choosing to check the box that says something like "prevent iDevices from syncing.". Then, I have found that it also helps to UNcheck the "sync new apps automatically" under the Apps tab (when the iPad is connected).
Oh, and somewhere there is an option to make iTunes NOT open automatically when the iPad is connected (you have to manually open iTunes). I forget where that is - and I'm not near my iTunes at the moment (if you can't find it - holler back and I'll take a look for it...).
With all those boxes checked/unchecked - my iTunes does nothing with my jail broken iPad3 until I tell it to. Makes life simpler because I really don't like iTunes (only use it to make backups and to store my apps).
So, double check all those options? Cause, again, my iTunes "behaves itself" with my jail broken iPad, so hopefully you've got a boxed wrong...
Marilyn