Since the eventual binary is in the local directory and HFS+ supports local calls, shouldn't you be able to just do
do shell script "VERSIONER_PERL_PREFER_32_BIT=yes `dirname "$0"`/target"
Just make sure that the applet binary is in the same folder as your crossover executable, with your plists adjusted to match.
For that matter, you don't need to use applescript to do this; I created the following file named launch:
VERSIONER_PERL_PREFER_32_BIT=yes `dirname "$0"`/target
and then did
sudo chmod +x launch
and it worked fine.
I renamed the binary in the MacOS folder to "target" and renamed the copied "launch" binary to the original target name.
Oh, and the lipo thing... it just strips out the PPC code, making the "fat" binary x86-only. It's smart enough that if there's code that's PPC-only, it won't strip it out; only strips the code that's available for both architectures. Doing this to quartz-wm forces it to run as x86 instead of PPC, which is what fixes the problems on SL. This stripped version should work just as well on any OS X running on an Intel Mac.
However, I'm on Vanilla Leopard, and after lipoing my quartz-wm, I'm getting the same circular ref thing as everyone else, even after reverting. I suspect something's cached somewhere, or a setting got modified during run. NONE of my wrappers work now.