To start, one thing needs to be made clear: Frank Gore is a great player and would contribute to any team in the National Football League. Undermining what a holdout on his part means to the team does not invalidate that in any way, it simply is how it is. Gore's ability as a running back will never come into question, the only knock against him lies in his durability, or lack thereof.
The most important thing to note about this holdout, which came at about the same time David Baas signed with the New York Giants, is that Gore isn't looking to "get paid." Well, that's not entirely inaccurate, he's looking for money, but spread over more time. He's entering the final year of his contract with the 49ers, and that scares him. Players at that point in their careers need stability and reassurance, and it's something that they often get.
But San Francisco doesn't have to break the bank for him, and when fans see the word "holdout" they need to be sure that they take a step back and realize that the guy (probably) isn't demanding millions and millions more at this point in time. Gore can assume whatever he wants about his value, but the market for a halfback with his injury concerns is small, and he's not going to get the money elsewhere.
Gore will be the main staple of Jim Harbaugh and Greg Roman's west coast offense, that much is clear. It's going to be a power running attack with a vertical game centered on the tight ends. Gore will make that offense run and run well, and the organization knows that.
In short, there's nothing to worry about with this. It's something that will get fixed sooner or later, unless Gore has somehow changed overnight and become insanely unrealistic, in which case we'll panic too.