The good news is that you can stop iTunes from harassing you about an newer (!), improved (!) version of the iOS Every. Time. You. Plug. It. In (can you tell it used to irritate me?
).
When you plug the jail broken iPad into iTunes and get that pop-up notice, you'll see that there is a teeny-tiny box in that pop-up - check it to tell iTunes not to give you that pop-up again. It'll still show on the main About tab, in iTunes, that your iPad needs updating, but it would take a conscious act to press that "Restore" button versu absentmindedly pressing an "OK" in a pop-up.
Do note that the pop-up will reappear when/if you load a new version of iTunes. Just repeat the checking of the box step...
Marilyn