I figured after Apple rewrote its developer agreement keeping apps created with Flash out, that the company would then remove all pre-existing apps created with Flash from the App Store. It turns out that either Apple hasn't gotten around to it yet, or the company has no intention of removing the apps since they're still alive and well.
A quick search yielded this page on Adobe.com, which highlights a number of apps that were created using the Flash "Packager for iPhone". I clicked through a bunch of them and they're still available for download, as of this writing.
The fact that the apps themselves are still standing on the App Store just feeds the flame of Adobe's argument. They're obviously not causing the iPhone any harm so did Apple decide that it just didn't want Adobe to have development control? It seems to be the case, at least at this stage.
It's definitely unfortunate that Apple is taking a stand to limit development environments like the Packager for iPhone. After all, in the end Apple makes money from every App that is sold on the App Store. If Apple really wanted to, it could require the development tool company to adhere to strict standards, but still allow the tool to produce an end package that would work on the iPhone.
For now the world will have to deal with Apple deciding what it wants to do. It's Apple's system, so if Apple wants to keep it closed, it can.