Hi Josh,
You sure you're not embarking on a slippery slope here? Trying to maintain patches for compatibility with every other Address Book extension out there might become a very time consuming process. Of course, I'm not saying you shouldn't try at all, just not spend too much time on it. You could obviously make exceptions for the most popular ones - or, you could just tell me to mind my own business...

Maybe an alternative would be to write some code to detect conflicts (extensions that modify the same code that gContactSync does), and have some decent error detection that will disable gContactSync and provide feedback that will tell you right away which extension is causing the problem (with as much detail as is possible), and maybe where the problem is best fixed (gContactSync, or, as appears in this case, the other extension) - then you could simply let the person reporting the problem report it to the other extension dev, so that it gets fixed in the appropriate place.
Just a thought, and my motivations for posting this are selfish - I'd much rather you spend your time improving gContactSync (and maybe coding the new extension to modify the QuickSearch to include the Organization field) than trying to work around bugs/conflicts in other peoples extensions.
Once you consider gContactSync feature complete, then obviously you could focus on compatibility with other AB extensions, and code workarounds if you felt it was worthwhile.