Killing long running MySQL queries is easy. There is KILL command
where PROCESS_ID is an ID from SHOW PROCESSLIST command.
I have created small PHP script to kill all long running processes using RegExp.
You can checkout it from my Github: https://github.com/klivan/MySQL-Process-Killer
Just change $host, $user and $password to access your MySQL server, and add regexp that matches your query.
Change $minExecutionTimeToKill to minimum number of seconds that query should be running before killing.
To run simply execute:
$ php ./kill.php
View on Github