tshunau,
I've done a lot of testing and am giving it to users today. The Application Setting method has not caused any issues so far, but Mustafa is correct in his concerns. You have to account for when, or if, Revit will crash.
I have it set so that if the variable is flipped on, it still will not proceed to scrub unless the file that I saved as the scrub file path (also an application setting) is opened. And only that file can be scrubbed.
So the greatest risk we face right now is Revit automatically opening the scrub file and starting to process it. Which is manageable. I saw this as easier to deal with than all the Journal backup files and the file management that this entailed, along with failure handling. But I do think that journal scripts had potential to really ease this process along had they been a bit more robust and supported.