hm, this is a very weary topic...
what i first notice is that your solution overwrites any already existent foo.pl.bak in that directory :(

a more general/recursive approach in a oneliner may be: find2perl . -depth -eval 'my $o = $_; s/\.pl$/$&.bak/ and -e or rename $o, $_' | perl -w

... or a 'rewriting' or your code:

#!/usr/bin/perl -w
use strict;
use File::Find;

my ($dir, $in, $out) = @ARGV;

File::Find::finddepth( {
     wanted => sub {
               my $o = $_;
               s/$in/$out/ or return;
               -e or rename $o, $_;
          }
     }, $dir );
[download]

heh, this latter version suffers ofc of limitation such as:
./kk.pl . '\.pl$' '$&.bak' ... which will not result in renaming 'foo.pl' to 'foo.pl.bak' but to 'foo$&.bak' :)

idea: do an engine to make possible specification of any 'substitution' pattern from the command line ;-)

--
AltBlue.