Apple's new App Store Developer Agreement has certainly spawned a hornet's nest of fury.
I expect it will be changed; it won't be the first time Apple has changed their mind and won't be the last. Despite Steve's comments I think there will be a modification at some point, if for no other reason than a big chunk of the currently successful app store games violate the new agreement (particularly everything that uses Unity3D). Killing a future irritant (the new Flash compiler product) is one thing, killing a 1000 developer products from mainstream publishers is another. Kicking all those 3D games out of the App Store would put a massive chill in the developer community, since there is no guarantee of success since Apple can simply change the agreement and toss you out. It's happened some, but never to big publishers and never to market leading applications en masse.
The right way for Apple to handle these is to qualify platforms (like Unity3D) individually so that they and their customers follow the necessary rules to make OS 4.0 work correctly. Sure Apple doesn't want to do this but in the end there will be too much pressure not to. This would make it easy to rule out Flash but not Unity3D. Arbitrary sure, but it's their platform.
The real test comes when existing apps which were built with Unity3D are released for the iPad. Will Apple kill them all? I can't imagine that; it's like shooting off your foot for a bunion, Not going to happen.
Check back in a couple months; maybe I will be right for once!