The 49ers' Peyton Manning blunder

Maybe it's already happened. But if it hasn't, I'd love to be on the phone when Jim Harbaugh calls Alex Smith to try to convince his quarterback that the 49ers' intense flirtation with Peyton Manning wasn't an indication that the organization doesn't have complete faith in the man who took San Francisco to the NFC championship game in January.

See, Alex, what had happened was …

This probably wasn't how Smith envisioned the offseason, after he engineered the 49ers to a stunning 13-3 season and to within three points of the Super Bowl.

Although until this year -- Smith's sixth in a 49ers uniform -- his tenure in San Francisco had been frustrating and disappointing, he proved this season that he can be a long-term answer at the game's most important position.

Only, the 49ers didn't reward Smith, a free agent, for his stellar play in 2011. In fact, they effectively dissed him as soon their pursuit of Manning began. And now that Manning reportedly will sign with the Denver Broncos, they're left to handle the fallout. That is, if they have the opportunity. Smith spent several hours on Sunday talking with the Miami Dolphins' coaching staff.

The collateral damage in San Francisco from the Manning pursuit is a glowing, neon sign that says this: The 49ers had no business being involved in the Manning sweepstakes in the first place.

Of course, Manning would have been an upgrade from Smith, who until the 2011 season had been considered a bust. Smith was the top pick in the 2005 NFL draft, but was 19-31 as a starter before last season. It certainly didn't help that Smith had to play for six different offensive coordinators, or that Harbaugh was his fourth head coach. But even on Smith's best day, he couldn't carry Manning's Gatorade.

Aside from the Patriots (Tom Brady), the Saints (Drew Brees), the Packers (Aaron Rodgers) and the Steelers (Ben Roethlisberger), there aren't a whole lot of teams for whom adding Manning wouldn't have been an upgrade.

But there is something to be said for chemistry, and togetherness. The 49ers' leap into relevancy can certainly be attributed to their outstanding defense and physical running game, but a big part of their success this season was their attitude. Harbaugh added toughness when he arrived from Stanford, but most importantly, he did a masterful job of making Smith see something in himself that very few others could see.

The realization that Harbaugh wasn't ready to cast him off like some incoming head coaches might have done performed wonders on Smith's confidence. In turn, the 49ers went from what many assumed would be a team bad enough to be in the running for one of the top quarterbacks in the upcoming draft (Andrew Luck or Robert Griffin III) to the verge of a Super Bowl. It sent the message to the players that they have a coach who won't give up on them easily.

Yes, the NFL is a business, but players still play on emotion and believe in naive principles. Smith's turnaround story is so rare, the 49ers owed it to him to show more faith in him than they did. Matt Schaub has been with Texans for five years, has yet to win a playoff game and missed a huge chunk of last season because of a foot injury, but Houston stayed away from the Manning circus – and, like San Francisco, the Texans appear to be a very slight upgrade away from a Super Bowl.

Now, the 49ers should legitimately worry whether they can recapture the intangible elements that made 2011 so special.

Smith might still re-sign in San Francisco, primarily because he'd be foolish to ignore the big picture there. With the additions of wide receivers Randy Moss and Mario Manningham, the 49ers have addressed their most pressing issue -- which wasn't quarterback. With the rest of the team basically intact, there's no reason to believe San Francisco won't again be in the thick of the Super Bowl conversation.

Smith reportedly already turned down a three-year, $24 million offer from the 49ers that included $10 million in guaranteed money. Now, he can expect the team to sweeten the deal. Nothing says "I'm sorry" quite like more millions.

But even with a financial apology, have the 49ers ruined their chemistry? Now that he has definitive proof that the organization still has some reservations, will Smith revert back to, well, Alex Smith?

After their victories last season, Harbaugh was often shown in the locker room yelling to his team, "Who's got it better than us?!"

And, on cue, everyone would yell back, "Nobody!"

If Harbaugh tries that routine next season, it's going to seem phony. Apparently, he and the organization believed they could have had something better at quarterback.