Another player would have to be put in for the position. They don't have provisions for a designated emergency back up. It is kind of like baseball. If you run out of pitchers, you bring in a position player and cope.
Actually they are drafting 9th, not second. That made them the 9th worst team in the league. They were tied with the Raiders and won the coin toss. Generally if the first stringer gets hurt, you would after that game have guys you could sign. Further, if you're down to your third stringer, you're hosed anyway. BTW the 49ers record over 2011-2013 was the best in the league. They also went to a Superbowl. They fleeced the Patriots out of a good QB for a song. And lo and behold they won several games in a row with him. Niners fans are saying Thanks Patriots. We love you!!! That is, until he loses a game. And given the QB sweepstakes occurring at the top, drafting 9 without the need of drafting a QB is a good spot to be in. They will be back.