If MySQL is consuming a lot of your CPU resources or is maxing out your server, the best thing to do is login and watch the queries in realtime.
Login to the server as root, and run "gp mysql login root" and then run:
And you'll see something like the following screen:
This screen will show which site is doing the query, and what it's doing.
You may also see table level locks, and if you do, you may want to consider switching to InnoDB, as it has row level locking instead of table level.