This is the thing.
From what the fella related in the article, it largely was the toddler learning to drive an obstacle course, getting to grips with controlling vehicles in a virtual setting. With the added extension, or motivation, of driving to help people. GTA is an open enough platform with which to do that.
If the father taught his kid in the game to steal a car, drive to the corner, score some smack then go shoot up, it would be a different matter. But he didn't ... soo ...
What he did do is allow his kid free reign in the GTA virtual setting, and it is fascinating to see how that ended up; from 2 points of view;
1. That the child was altruistic, entirely of his own accord and without prompting from Dad
2. That GTA was open enough to allow the child, when given free reign, to be altruistic.
I agree I would be a little uncomfortable with this 'experiment', but it is what it is, and I see no harm as having come to the child now that it has taken place.
As Zig asked, what harm do you see as having come to the child. Not what might have come.