You made me ponder, after I read this last night, the effect of his mother's death on John. I think that perhaps that scene was intended to show the beginning of his isolation, because such a massive trauma would have lasting repercussions. His mother died right next to him, as he waited while beset by injuries for rescue. I think this is when he started to withdraw from genuine connection, leading to the Agent Sheppard we meet at the start of the story, who has fairly breezy interactions with coworkers. He's found a way to cope (charm) that still keeps people at a distance. Which of course feeds into Rodney's abrasiveness as a mechanism to get behind John's barriers.

I do think that his mother's death could have been touched upon again in a way that made its influence stronger.