Source filters are only evil if you invoke them, the beauty of smart comments is that normally they're just comments. Just leave 'use Smart::Comments' out of your code, then to invoke the smart comments (and the source filter), invoke your script via:

perl -MSmart::Comments myscript.pl
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or for finer control:

perl -MSmart::Comments='####' myscript.pl
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See Smart::Comments for details. This way you have zero overhead except when debugging. I'm surprised this simple technique isn't mentioned in the documentation.