Успях.
Създайте файл kill_sleep.sh
mysql -u<user> -p<password> -h<host> -e "select concat('KILL ',id,';') into outfile '/tmp/sleep_processes.txt' from information_schema.processlist where Command = 'Sleep'"
mysql -u<user> -p<password> -h<host> -e "source /tmp/sleep_processes.txt;"
rm -rf /tmp/sleep_processes.txt
И задайте kill_sleep.sh на cron задание.
