The error is constantly made by opposing defensive coordinators, defend the pistol as you would defend the read option, but the problem is the pistol isn't the read option, that's just one of many formations the pistol mimics.
In this piece, I attempt to help by giving those who don't fully understand the pistol offense a better understanding of why it's nearly impossible to defend with the right player personnel, like the 49ers currently possess.
First of all, unlike the read option, the pistol mimics other formations in the blink of an eye.
In fact, it mimics the shotgun, air raid, "I" and pro-set formations, and the read option. It makes defending this offense nearly impossible with the right starting group of players. The 49ers have Kaepernick, Gore, Crabtree, and Davis just to name a few offensive weapons in this set.
Here's why the pistol is more dangerous than the read option: The standard read option (Redskins and Seahawks), maintains any defender can make the correct read to stop the play. The pistol offense is much harder to defend, because it can go from the standard shotgun, with running back lined five feet behind, to a perfect mimic of any of the major formations used in the game. Just the snap alone can spell defeat for a defense guarding the pistol with the right set of players.
Nevada's former coach Ault created this master piece to ensure one huge advantage the read option doesn't offer, a constant 11-10 advantage to the offense. The 49ers are led by the-dual threat and big size of Kaepernick, the speed from the backfield of Gore and three good receivers, mainly Crabtree and Davis -- much like during Kaep's days in Nevada with Wimberly and Green respectively, and Taua in the backfield.
The 11-10 advantage, comes from the pistol forcing the defense to use a single defender on each play that they can't afford to lose, to spy on the dual-threat quarterback on every down, which in effect only works on downs where Kaep runs the ball.
Otherwise, the 49ers' offense owns the advantage by looking off the spy and passing it deep for a big gain, per the spy not being in coverage, or a big run play, as the spy can't cover both Kaepernick and Gore at the same time and only has a second to respond once the ball is snapped.
That 11-10 advantage is usually spotted by the quarterback, who then calls the mimic route, and the play shifts from the pistol to a clone of any of the major formations once the ball is snapped, leaving the defense at two major disadvantages off the bat, and the 11-10 disadvantage when responding to the mimic formations the pistol quickly turns into to complete the play.
A team utilizing the pistol offense doesn't require the best defense in the league, because the offense is nearly impossible to defend, unless the offense just plainly doesn't show up on game day. Even then, it's still a 11-10 nightmare for opposing coaches to properly prepare for, and the weapons the 49ers have on offense makes it that much more difficult.
Six of the last eight teams learned this lesson the hard way since Kaepernick was named the starter and Harbaugh installed the Ault-style pistol offense, that allowed Kaepernick to set NCAA records that won't be broken anytime in the near future, except for perhaps Cody Fajardo. However, coach Ault decided to retire and with him his picture perfect offense at UNR.
There's only one defense to the pistol with the weapons the 49ers have, spy and pray the offense doesn't show up, because even the top defenses in the NFL struggle against a constantly mimicking formation. Outside of that, the only way to win is by the opposing offense doing the same by scoring at will, but the moment they fall of the pace, the pistol offense has sealed the game, as was seen last week when the 49ers upended the Packers.
The Packers did get close during chump time, but by then the outcome was mathematical, just like the formation itself. It's nearly impossible to defend, because it's impossible to prepare for other than best-guess estimate, which give the 49ers the advantage heading into the NFC Championship game.
There is a huge difference between the read option and the pistol, the quicker the media and coaches can adapt, the quicker they can understand why this formation is more advanced than their ability to currently present an adequate defense exists, other than spying and giving up to 11-10 advantage to defend it on every offensive down.