I punched out a quick graph showing the Average Per Year Salary (APY) of the top 50 cornerbacks and safeties in the NFL. The blue vertical line represents Carlos Roger's contract with a tick showing the median starting APY of that position (defined as the 32nd highest contract). The red vertical line represents Donte Witner.
Even with his flaws, I feel that Witner is still a starting caliber safety. The cost to resign him will probably be close to around what he is making right now, and definitely on the value side of the exponential curve.
EDIT: After some discussion with other NNers, I don't think we will be bringing back Whitner. This FA period is probably going to be Whitner's last chance at a big contract. (He's 29 and is in the tail end of the prime of his career). I discounted his value because of his weakness in coverage, but if you look in the list of the top 16 paid safeties, there are many who are known for weak coverage skills. We were able to get Whitner for a discount because of the disappointing start to his career in Cincinnati. I think it is likely that he will be able to get top 16 money from a team that is desperate for some safety help (see Goldson), that would put his price tag at above $5M per year.
For Rogers, on the other hand, it's debatable if he is a starting corner back anymore. Even if he restructured his contract, I'm not sure if it would be worth it for the Niners. The Niners can possibly save $5 million in cap space and sign someone to fill his position for less than $4 million.
Unless there is a complete steal in the draft at safety, I'm guessing that the Niners will try to keep Witner for another year or two to maintain some continuity in the secondary. That will give Reid another year to become the leader in the secondary before he is ready to groom Witner's replacement.