I was able to repeat this using Tom's test case. It looks like pt-kill will succeed on killing the first query, but all subsequent queries it will fail to kill on "MySQL server has gone away" at /usr/bin/pt-kill line 6806. And it looks like it won't reestablish the database connection until the next "SHOW FULL PROCESSLIST" fails after the two failed kill attempts.
I was able to repeat this using Tom's test case. It looks like pt-kill will succeed on killing the first query, but all subsequent queries it will fail to kill on "MySQL server has gone away" at /usr/bin/pt-kill line 6806. And it looks like it won't reestablish the database connection until the next "SHOW FULL PROCESSLIST" fails after the two failed kill attempts.