Well you could hypothesize that that's where it's going, but at the moment, they're going to allow signed, non-app-store apps by default as well. All a dev needs to do now is to sign their binary when they build it and problem solved. I can't see why anyone actively maintaining an app wouldn't make the small change required.
Even if you sign the binary, you are still getting shut out of the market for the segment of users that select App Store only. You pay Apple the App Store cut or you limit your market... not a great choice to have to make.
