In that case, dig into wakaba.pl's process_file function, and look for if($md5), where the existing MD5 checks are. If you want a quick hack, add something like this:
my %banned=(
"12345abcd67890..." => 1,
"44332211fedcba..." => 1,
);if($banned{$md5})
{
unlink $filename; # make sure to remove the file
make_error("Enough of THAT");
}