What I just don't get is why people even bother JB'ing, IT VOIDS YOUR WARRENTY.
Well, you do at your own risk but I had no problems with Apple claiming warranty replacement on an iPad 2 that had been jailbroken before. They even did a scan of it and it didn't come up. They were mostly interested in if I had ever replaced the glass on the screen, and were looking that over under a black light (kind of had me intrigued as to what they were looking for).
Anyway, so long as you restore to their firmware you should be ok and not have to fear an Apple "Genius" calling you out.
In some rare circumstance where you brick your device and are unable to restore the firmware the burden of proof is on them to show that you were messing with it or trying to hack it.
There may be a day when Apple may just flag your account for JBing activity. It is possible for apps such as the DirecTV app to detect that it is on a JB iPad and then refuse to work. It really wouldn't be difficult for Apple to implement similar functionality into App Store (refuse to work) and then flag your account for JB activity. I hope it never gets that extreme... but if we are back at "this is illegal to do on this hardware" then it might be enough for Apple to implement that kind of functionality into iOS.