Nelson should start the rest of the year.
I fail to see what Gray can offer at the position that Nelson can't do, and that's after ONE start. I'm not even sure I agree that Gray is a better runner. He's stronger, and he can probably push the pile a little better, which is something I DON'T want my QB doing anyway. In just his first career NCAA action, he already showed an ability that Gray never seemed to grasp; when under pressure, moving in the pocket to buy time and find a receiver downfield. In the few occasions he did that, he wasn't always successful, but at least he gave the play a chance instead of taking off for a 3-yard gain on 3rd and 8. Nelson actually looks a LITTLE bit quicker than Gray running the ball, a tiny bit more shiftiness.
Bottom line, it all goes back to the O-Line. It's a dumpster fire right now with the injuries and youth. I think they can still put together some drives the rest of the way and hopefully get bowl eligible but I doubt we see much consistency out of the offense regardless of who's under center.