They've already demonstrated that they have the means to inject into a binary stream, so unless Apple start encrypting everything - and I mean, everything - that happens between the App store and dragging the App into /Applications, there's little we can do to resolve this issue.

This is one of those cases where the betrayal of the NSA/GCHQ/Spy-Agencies-of-the-5-eyes-nations is really obvious. We can no longer trust our developer tools...