Interesting. Let's say I'm a developer writing a Bittorrent client. Do I leave it unsigned and get lower adoption because people are afraid of malware, or do I sign it and hope that Apple doesn't someday revoke my key?
Of course, Apple could have done this before. They could push out an OS update that wiped an app from everyone's computers. But that was a huge undertaking and now they have a process that is generally accepted from the App Store, and I wouldn't be surprised if we start to see it more regularly.
Edit: Apple wouldn't even have to be against Bittorrent clients. They could just get sued by record labels and lose, and then a judge would say "You built the capability to remotely disable apps, so use it to disable this one."
Practically speaking, I don't see this being much of a problem. If Apple does disable your app, but your app is not malicious and users actually want it, they can just return to your site and download an unsigned version. This would be a minor annoyance to your users, but if you are having the kinds of troubles that cause Apple to disable your app, you probably have much bigger things to worry about than a few thousand customers downloading your app again.
Are you making the assumption that people would be afraid of your application because it could potentially be malware, or because they don't want to switch to the third mode? If it's the latter, I hope the control is on an individual applications basis so that I am alerted about other unsigned applications even after having allowed yours.
If it's about the first, I think the users who can get a Bittorrent client up and running (and have an interest in it, in the first place) are also able to read reviews and ask friends who may have recommended them this application.
Of course, Apple could have done this before. They could push out an OS update that wiped an app from everyone's computers. But that was a huge undertaking and now they have a process that is generally accepted from the App Store, and I wouldn't be surprised if we start to see it more regularly.
Edit: Apple wouldn't even have to be against Bittorrent clients. They could just get sued by record labels and lose, and then a judge would say "You built the capability to remotely disable apps, so use it to disable this one."