We, the viewer, are supposed to forgive John for his understandable rage, and subsequent violence because of it - for the same reason Mary (et al) forgave Ajay his rage and his subsequent violence. Both John and Ajay are 'tortured' souls, lashing out blindly at a malevolent universe which has inflicted so much senseless pain on them - taken away love and family from them. They both live in horror nightmares. The way to save their souls is to get them past their horror and rage, and on to healing. To make them understand they are loved.
It is not a coincidence that both episodes involved such similar situations and responses. And the reason for both of them was to set up for the third - and final - similar situation and response: Eurus - who is also an existentially tortured soul, deprived of love all her life,and lashing out with incredible violence at a horrific universe. She, too, needs to be saved.
Basically, as Benedict stated, the theme of the season is: "Love conquers all"