I don't see how Adobe would be any different from MonoTouch or the Unity Game Framework. Given those apps are allowed I don't see how Apple could reasonably ban Flash apps (other than "to further hurt Adobe")

I guess there is a danger for developers in that they could spend time on their app only to have Apple arbitrarily decide to ban all Flash apps. But the question is whether that danger is any bigger than the danger of Apple arbitrarily banning your app for some other benign reason.