It looks like Apple's war against Adobe Flash is
The use of a cross-compiler like Adobe's will leave telltale signs in the final code that Apple could easily recognize. Some developers have no choice but to alter their development methods if they intend to put out an iPhone or iPad app. Any work already done in other languages may as well be scrapped, leaving the poor dev back at square one.
This leaves Adobe in a strange place. The Packager for iPhone was supposed to be a big feature in the upcoming Flash CS5. The license was just made available with the new dev preview today, so we'll be interested to see how developers react to this.