Relax jailbreakers, it is just a patent for now.
Since jailbreaking really got easy a lot of iPhone users roll on the Apple unapproved side of things. Apple sees a lot of value in the closed and controlled eco-system. The Register reports that Apple filed for a patent with the title "Systems and Methods for Identifying Unauthorized Users of an Electronic Device". From a legal standpoint jailbreaking has been cleared recently. Apple paints a broader application for the patent that sees also value in protecting owners of devices from hackers.
I am not sure if Apple would be able to get away with a kill switch for jailbroken iPhones. The community outcry would be dramatic. As said above for now this is just a patent application.