With several players -- Colin Kaepernick, Aldon Smith and Michael Crabtree -- all figuring to command big deals in the next year or so, the 49ers have to be smart about their overall spending. They can't get too crazy with their free agents this season.
But with that said, Whitner is an important piece. He had a good season in 2013 and his three seasons (he signed as a free agent in 2011) with the 49ers have been a success. He is good in the locker room and his aggressive play is a good fit with the defense.
Also, there's the fact the 49ers don't have any young players who can replace Whitner. This is a deep program overall, but there is no one the team can count on to replace Whitner if he leaves.
They could always draft a young safety as they did last year with first-round pick, Eric Reid. That worked well. Reid made the Pro Bowl. But the 49ers are probably better off going with Whitner for a few more years. So, while it could be tough to re-sign, keeping Whitner may be in the team's best interest.