Well... the firs one (with kill) notifies that the process was killed, while with the second solution you have to wait for 2 seconds after the program has finished :-)
I suppose that if you really want to cover that message in a bit more polite way, maybe try something like this:

END { print "Cleaning up...\n"; close STDOUT; close STDERR; }

Normal user would think that it really does something and it's not sleeping any way ;-)
IMHO the best way to avoid original message is to pay for perl2exe - if you really need it.