vincent is right, kill -9 stops processes suddenly and doesn't give them a chance to clean up nicely or stop what they're doing.
andrew did say "I don't have my password so I don't have priveleges to stop MySQL" which implies he doesn't have root access.
resetting the unix root password is simple and only takes a minute or two if you're sitting in front of the box. assuming lilo is installed just reboot and at the lilo prompt type "single". now run "passwd root" and change the root password. failing that, mount the drive on another box and replace the password in /etc/passwd or /etc/shadow with a known password in encryted format. not sure if cobalt has their own way to boot into single user mode.
assuming he does have the root password and can stop mysql, then andrew needs to read the manual:
http://www.mysql.com/doc/R/e/Resetting_permissions.html