I've experienced something yesterday that's related to what's mentioned in this article. I think Apple has the ability to block specific iPhone users from running third-party applications that were previously downloaded from iTunes and installed on the device. Let me explain what happened, and then you can develop your own conclusions on what was going on.
Prior to this story, I've had two third-party apps running on my phone: Facebook and Last.fm. Last week, I received an email from Apple that my iTunes billing data was out-of-date and needed updating. I ignored the email because I don't purchase music or apps on iTunes (though I will download free apps). After that email, I couldn't download new apps (even if they were free) until that data was updated.
This is where it gets interesting: Yesterday, I noticed that both of my third-party apps could not launch from the phone at all. I figured it was a bug and that I would wait until I get home to install the 2.0.1 update, and if that doesn't fix it, re-install the apps. Well after I get home and update the phone, the third-party apps are still not working. I delete Last.fm and attempt to reinstall. I am prompted about the billing data still being out-of-date so I comply with their demands and I finally get Last.fm installed. It works, and even more curiously, Facebook works too even though I didn't bother re-installing that application.
So here is my conclusion: It appears as though my ability to run certain applications on my phone was suspended until I could update the billing data on my iTunes account. It wasn't until when I provided new billing information, that my third-party apps could run again. While the article above mentions blacklisting specific applications from everyone, it seems as though Apple can also block specific users from running third-party apps (maybe even specific apps) even after they've been purchased and installed.