Maybe it's a cultural difference I don't understand but the guy had enough successful ideas that I think Nintendo would obviously still benefit from his contributions.
I think you're right, because I remember reading stuff about Japanese samurai warrior codes how if you failed you were supposed to kill yourself, and that's quite a bit different than how we treat people who fail here in the west. Of course the Samurai days are gone, but parts of that culture probably live on in their business ethics.
But I think Gunpei's spirit lives on in Iwata. If you look at the two men you see a lot of similarities, and the DS which Iwata designed is very similar to the innovative philosophies that led to the Virtual Boy (albeit infinitely more successful). And to be fair, I very strongly believe the VB probably could have become successful if it had more support thrown behind it. Usually Nintendo has to lead the way and develop stuff themselves before others climb aboard, but they didn't really do that with the VB. There wasn't really a single major franchise present on the system, and Gunpei can't really be blamed for that.