49ers keep the faith in Alex Smith

Despite the vehement denials of head coach Jim Harbaugh, the San Francisco 49ers are perceived to have fallen short during the free-agent bidding for Peyton Manning.

The reality is that the franchise may be better off for sticking with Alex Smith regardless of whether Harbaugh is telling the truth or doing damage control.

Such a statement would be considered preposterous not too long ago. But that was before Manning’s health problems and Smith’s improbable 2011 rise into becoming a quality starter.

It’s still too early to tell whether the 36-year-old Manning can regain his previous Hall of Fame form following four neck surgeries. The comeback attempt continues at 4 p.m. ET Sunday when Denver — the club that won the offseason Manning sweepstakes — plays the 49ers on FOX.

As for San Francisco, the 49ers know for certain that they still field one of the NFL’s most mentally tough quarterbacks coming off his best season. They also believe the 28-year-old Smith may have even more upside in 2012 thanks to an improved supporting cast.

Still, there is pressure on Smith to prove the 49ers should have never pursued Manning in the first place.

Not that Smith will let this affect him. He has survived far less favorable scrutiny than being compared to a passer of Manning’s standing.

Smith’s NFL career was declared dead so frequently during his first seven seasons that nothing remained on the carcass for media buzzards to scavenge. San Francisco’s decision to re-sign Smith in the 2011 offseason was widely panned. If the 49ers were to start anew under Harabugh, cutting ties with a player whose struggles greatly contributed to past failings seemed like it should have been a no-brainer.

Instead, Harbaugh was the one proven sage.

With full support of the coaching staff, a dominating defense and a more diverse offensive attack that took advantage of his strengths, Smith began to prosper like the 49ers expected when making him the No. 1 pick in the 2005 draft.

He wasn’t going to carry the entire offense a la Manning in his Indianapolis Colts heyday. That’s a major reason why Smith didn’t draw anywhere close to Manning-like interest in free agency during the offseason. But it’s also not what Harbaugh demanded. Smith was efficient, avoided interceptions and came through with clutch performances in big games leading to San Francisco’s surprising run to the NFC championship game.

“When you look at the turnover ratio and how well he protected the ball, it says a lot about the decision making,” said 49ers general manager Trent Baalke, referring to Smith’s 17 touchdowns and five interceptions in 2011. “A lot has been made about cautiousness and the system protecting him. We don’t buy that. I think it’s the evolution of him as a person — getting comfortable with the system, understanding when to take chances and when not to.”

One thing that hasn’t changed: Smith’s unflappable demeanor. Even when he was floundering under prior coaching staffs and different offensive coordinators, Smith maintained the respect of his 49ers teammates by not blaming others and continuing to work diligently at getting better. Smith also appears nonplussed by San Francisco’s courting of Manning and subsequent delay in signing him to a new three-year, $24 million contract.

“There are definitely hard times for sure,” Smith recently told FOXSports.com after a 49ers training camp practice. “You’ve got to come to work no matter how tough or great it gets and be the guy who doesn’t change. You’ve got to stay grounded. I take a lot of pride in that.”

Smith’s teammates are proud of how he has persevered.

“Alex has come a long way,” said 49ers tight end Vernon Davis, who was Smith’s roommate for the past two training camps. “I look at Alex as one of the strongest people I’ve ever seen. I say that because he’s been on a rollercoaster. He’s been through numerous offensive coordinators, but he always managed to hang in there and keep his head up high.”

Newfound prosperity under Harbaugh didn’t change Smith’s approach either.

“Everybody in the media is like, ‘What’s changed in Alex?’” said 49ers left tackle Joe Staley, who is one of Smith’s closest friends on the team. “I always say nothing has changed. We have a coaching staff putting us in great position to make plays and we’re really on top of our stuff. Overall, the execution on offense is better.

“Alex has really come along with his tells and knowing every single position. But as far as him being a different type of person, he’s not.”

San Francisco’s 2012 offense is a different story.

The 49ers upgraded at wide receiver after the injury-plagued unit’s miserable showing in the overtime NFC title game loss to the New York Giants. Randy Moss has shown signs of being a bona fide deep threat once again after spending last season out of football. Super Bowl XLVI hero Mario Manningham and 2012 first-round pick A.J. Jenkins of Illinois were added to a group that already featured two former Top 10 draft picks in Michael Crabtree and Ted Ginn Jr.

A strong running game also received a further infusion of talent with a bruiser (ex-Giants starter Brandon Jacobs) and a speedster (rookie LaMichael James) joining the one-two punch of Frank Gore and Kendall Hunter.

Smith thinks such pickups should help his offense achieve its goal of being more consistent in red-zone and short-yardage “situational” football. Davis believes that the 49ers might not have fallen short against the Giants had these pieces been in place last season.

“Maybe we were missing a few pieces like Moss and Manningham,” Davis said. “We had some guys on the team who could get it done, but we had injuries and probably needed a little more.

“The most exciting thing is we have a little more now. We have a lot to look forward to.”

That’s why it’s best to wait before making a final judgment on whether the 49ers should have tried even harder to sign Manning.