Golson had at least two big runs that I remember right up the middle, one of which he got tattooed on and had to come out of the game. You don't make those playcalls if you are overly scared of your QB getting hurt.
I'm not saying he was Colin Kaepernick (nor remotely implying he was) but I don't think the facts back up that Kelly restrained him more after the Stanford game. Sneaks or runs with the goal of getting out of bounds still put your QB at risk (though lower) and if he was really scared, he wouldn't have called so many relative to the first half of the season.
