Suetonius:

74 Even in avenging wrongs he was by nature most merci­ful, and when he got hold of the pirates who had captured him, he had them crucified, since he had sworn beforehand that he would do so, but ordered that their throats be cut first.

https://penelope.uchicago.edu/Thayer/E/Roman/Texts/Suetonius/12Caesars/Julius*.html

Caesar was capable of great callousness, but you don't see him engage in casual or impulsive cruelty or blow his top like some other historical figures. He was in general a very calculating fellow, and very attentive to his reputation. Furthermore, reciprocity was highly valued in the Classical world, and it's likely that Caesar felt obliged to show some form of lenience since the pirates had humored him while he was a captive.