I love a good conspiracy theory and all, but there are several flaws here.
1) Killing an authorized user's device would run afoul of a great many laws here and around the world I would think.
2) Notice the patent talks about the Identification of hacked/jailbroken devices in reference to theives. As in, steal an iPhone, hack it to get it to work. Apple ID's it, and kills it.
3) IMHO, Apple doesn't care as much about jailbreakers as people think. If they did, it wouldn't take an average of 1.7 days for a new version of iOS to be hacked.