The fact that there is now news about Hayne's pass protection skills means that he is definitely in the conversation about being the 3rd down back. Bush's injury couldn't have come at a better time for Hayne and the fact that the 49ers appear comfortable with using Hayne in Bush's role whilst he is injured is a good sign that he might stick on the roster.
That being said, the 49ers are definitely going to ride Carlos Hyde all the way in the rushing game, and that appears to be their template for games so far. I know it's hard to project schemes off just one game, and the Vikings were horrible against the run, but that's the way it looks to me.