mysqld constant CPU usage when absolutly nothing is connected and no queries
Yes, your kill statement is the likely cause.

The command SHOW PROCESSLIST will only show you what is happening in foreground threads.  InnoDB is likely rolling back the transaction in the background.  Some diagnostics you might find useful:


SHOW ENGINE INNODB STATUS - see what is happening inside of InnoDB.  Under 'TRANSACTIONS' you should see your killed staetment being rolled back.
SELECT * FROM performance_schema.threads - show all threads in MySQL.
MySQL Workbench 6.1 includes Performance Schema Reports, exposing some of this data in a visual form.