The reason Joy killed the Knights was because they were very weak and had a very weak constitution they were of no use to him in the Kingdom of Twilight. The reason he killed ghosts who were related to Knights was purely out of precaution he did not want someone coming after him for something as futile as revenge.
The growth of ghosts depended on their will whereas for humans it depended on their will as well as light space. The Knights from Lucifer's army did not have that great will because they did not face many hardships. Lucifer was like a God to them and because of it, their will was always about belief in Lucifer rather than the self. Also as they were born on the outskirts the light essence which they consumed was average. Even Lucifer whom they treated as God was just an above average Knight by the standards of Twilight Empire.