Nothing to worry about
It wasn't long ago when the back door to remove Apps was widely talked about, but Apple has yet the need to use it. Even when Apps that have been purchased legitimately off the Apple store that allows users to do things they shouldn't be able to do. Like the "Flashlight" app.
I see this as a way for Apple to help control issues like hackers taking advantage of iDevices and potential security flaws. Also if something gets out of hand from a "corrupt" app that does get leaked thru, that is malicious, gets lock so it becomes an "unauthorized" user/app. Not removing the App but just disabling some of the functions.
There are lots of reasons why Apple could be using the methods they are implementing and as of this moment I see no reason to worry about Apple's intentions. If Apple tried to use this as an Anti-Jailbreak then Apple will instantly be sued as jail breaking is now a legal right.
I am not naive to think people can't abuse power, including Apple, so being aware is great, but being negative doesn't help either. I have not seen Apple abuse personal privacy yet, only the opposite. Apple has, in my opinion, gone to extremes when you start looking at what other companies are doing with our personal information. Facebook is so unsecure it is scary yet I don't see people raising arms about them.
I see this move as another way Apple is protecting me and my personal information.