How do you know Hughes was unconscious first? I seriously doubt that. Newton didn't drop out of his arms. Hughes must still have been conscious when he started the slam.
Anyway, let's even say (for the sake of argument) that the ref had stepped in and said Newton won. In a fight that close, and that exciting, and with Newton stone cold KOed after "winning," there would STILL be a rematch. So the overall effect of the decision was zero for MMA history. Maybe it affected Newton's purse, but that's about it.
I think in the first fight we got to see a totally focused Carlos Newton who had trained everything perfectly.
In his subsequent fights he had either been training too much of one thing and not another or he was spreading himself out too much with non mma stuff.
I think Carlos is a great fighter with a heap of natural ability but he has to focus on it to do his best.
Here's hoping Carlos takes some time off to do other things and comes back with a vengeance.