Am I bad person for mixing shell and perl this way?

Nah. But quicky scripts have a way of escaping into the wild, where people become dependent on them and howl when they break. That's one reason to do more in Perl.

Consider changing     my $key=`cat $file`; into

    open(K, "<$file") or die "$file: $!\n";
    my $key = do { local $/; <K> };
    close(K);
    chomp($key);
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Doing it all in Perl protects against someone having a cat in an unexpected place in their PATH.