2012-04-16, 05:40 PM
A different approach might be to rebuild the launch services database, so that it would no longer associate OmniFocus with the downloaded version, but rather the MAS version. I'm assuming here that a tell application "OmniFocus" block will direct the MAS version if the other has never been installed and launched, but don't have any way to verify it, having no MAS apps where I also have the non-MAS version. Seems crazy to have to edit a bunch of scripts!
I know Onyx and TinkerTool both have commands to rebuild the database. It's just a guess that this will fix the problem, but it might be worth trying before breaking out the editor, if you've got a bunch of scripts you'll have to edit.