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I'm also on 10.6.6 and the AppleScript has been working for me for the past couple of months and again when I used it yesterday.
I used to have the standard Python 2.6-ish install, but then I went and got the 2.7.1 installer from Python.org (after the source failed to compile, grr).
Maybe your unzip utility sets the permissions wrongly?
In any case, to use it on the command-line, just do python PATH/TO/kindlestrip.py OriginalFile.mobi OutputFile.mobi OptionalStrippedData.zip
You can drag and drop the kindlestrip.py file onto the Terminal window and it will autofill its path, and the 3rd filename is optional if you don't care about looking at the stripped data.
You can also alias it in your .profile for convenience, aka:
alias kstrip="python PATH/TO/kindlestrip.py"
and then string together a series of commands to batch process a folder:
alias kstripbatch='for m in *.mobi; do kstrip "$m" "${m/.mobi/-stripped.mobi}"; done'
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