It's an area that demands a lot of experience and patience. The Niners have a good history with veteran free agents (Clements, W.Harris, Bly, M.Lewis, Roman), all of whom stepped in and made an immediate impact. Drafted players, on the other hand, have taken at least two years to get playing time (S.Spencer, T.Brown, Goldson), and even then it's no guarantee that they'll be consistent starting-quality players.
As much as they need a safety, I'm hoping they can find one in free agency. Save the draft for the offense and pass-rushers.