I'm the developer of the LaTeXTools plugin, and this post just made me very sad
I thought the days of worrying about OSX's silly way to handle env variables were behind me..
Well, no matter. Fix #3 (changing the sublime-build file) won't work because the build command is actually a custimized version, and I don't think it currently reads the env variable at all. BUT, this is definitely something I need to fix.
I've been drifting away from OSX lately (can't stand Apple's attitude to "competition" anymore), but I do have Macs in the house. On the other hand, none of them is running Mountain Lion, and I actually wasn't planning to "upgrade" (not clear what's in it for me). I'll do my best, but I can't give an ETA.
EDIT: the quickest fix would be to actually read the env variable in sublime-build. Then, you could just copy the sublime-build file to the User directory. Whatever ST2 finds there takes precedence over any plugin-specific file, so even if the plugin's sublime-build gets clobbered, it doesn't matter. Again, no ETA, but this may be the easiest (though not the cleanest) fix.