I'm very thankful for Roddenberry's creation, but there are times he really to let the writers tell their stories.
The story got hamstrung because he declared that children in the future would accept death easily and then move on. Piller and Moore obviously didn't like that idea because it makes these characters difficult to understand and accept. Moore elaborates in the commentary that the alien angle was added to bring the mother back instead of Jeremy using into the holodeck to escape from the reality.
I guess the idea of escaping to the holodeck remained in the minds of the writers and adapted it for Barclay in Hollow Pursuits. If damaging the story of this episode gave us Lt. Barclay, then I'd say it was a good deal.
In the commentary, I think Moore said he was happy with the kid, but I think he was just being nice.