Just apply a RewriteCond that says NOT /cgi-bin/blah first. Then the RewriteRule will only get invoked on the first pass, not once it has been done (untested)...
There are also other hooks to prevent looping (they let you see it this request is a subrequest of the original) but that should do the trick.
RewriteCond ! ^/cgi-bin/myscript.pl.*$
RewriteRule ^(.*)$ /cgi-bin/myscript.pl?$1
cheers
tachyon
s&&rsenoyhcatreve&&&s&n.+t&"$'$`$\"$\&"&ee&&y&srve&&d&&print
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