We can manually stop the unwanted MySQL query process using mysqladmin command,

Step 1 : Check the query process list,

# mysqladmin processlist;


+---------+------------------+----------------------+------------------+----------------+------+---------------+------------------+

| Id      | User             | Host                 | db               | Command        | Time | State         | Info             |

+---------+------------------+----------------------+------------------+----------------+------+---------------+------------------+

| 72      | eximstats        | localhost            | eximstats        | Sleep          | 45   |               |                  |

| 3770271 | linuxfaq_thelinux | 192.168.1.10:45453 | linuxfaq_thelinux | Sleep          | 3490 |               |                  |

| 3770276 | linuxfaq_thelinux | 192.168.1.10:45466 | linuxfaq_thelinux | Sleep          | 3490 |               |                  |

| 3770281 | linuxfaq_thelinux | 192.168.1.10:45471 | linuxfaq_thelinux | Sleep          | 3490 |               |                  |

+---------+------------------+----------------------+------------------+----------------+------+---------------+------------------+


Step 2: kill the process PID

 mysqladmin -u root -p kill  PID 
 
# mysqladmin -u root -p kill  3770271

If you dont have set root password,
 
# mysqladmin -u root kill 3770271