The comments in a sql file will be probably either at the start of the line with or without white spaces "^\s*--" or after a semicolon "\;\s*--". If I'm not wrong, this is not a valid sql sentence in most databases, thus you shouldn't have it:

(And you shouldn't have tables with name fields beginning by "--")

Something like this should be enough to strip all comments from your file:

open my ORIGINALFILE, '<', 'file.sql' or die... etc
open my CLEANEDFILE, '>', outfile... etc, as usual
while (<ORIGINALFILE>){
  next if /^\s*--.*$/   ;
  s/\;\s*--.*$/;/       ;
  print CLEANEDFILE $_       ;
}
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