Thanks for listing these side effects -- while I have listed most of them in Service Scrubber's "Read Me" file, repeating them is a good thing, as most users don't bother reading "Read Me" files...
;-)
And to be honest, I've never even thought of the third one.
As far as creating a haxie for the same purpose is concerned, I agree that this would be a good solution for users who don't want their info.plists edited. Here's a couple of reasons why I didn't do it that way:
1. Some users don't want haxies on their computers. (Me included, BTW, but that's just my personal preference. I'm not saying that APE is a bad thing. In fact, it's the most elegant way of doing some things.)
2. Unsanity's application enhancer SDK is $100 for developers. While that's not exactly a major investment, you don't want to rely on a framework that (i) is not free and (ii) might break on future OS X versions when you're releasing software as free-/donationware.
So there you have it. Thanks again for pointing Service Scrubber out!