As mentioned, Dooku had been disarmed and executed instead of killed in combat, however he was still a threat due to his force powers and the fact Anakin was alone with an important hostage and his unconscious master in an enemy ship.
It seems similar to this thread in terms of the situation Anakin was in.
Is it "the Jedi way" to kill a defenseless being if they pose a sufficient threat?Is it "the Jedi way" to kill a defenseless being if they pose a sufficient threat?
