OMF: Shinji cringes at the very thought of violence. Couldn't Toji just write a formal apology or make do with some other non-violent act of contrition?!
Reichu: Well, this IS Toji we're talking about! Is Toji even capable of writing? :lol: (But I kid.)
Incisivis: That Shinji doesn't want to punch Toji is yet another indication that Shinji is not a "typical" teenage boy. He can't understand the connection between punching and atonement, the sort of male-bonding-through-mild-violence that we in the West recognize as a clap on the shoulder, an elbow in the side. It also ties into Shinji's dislike of violence at this point in the series.