The decision to play Aldon Smith against the Indianapolis Colts before sending him into rehab was questionable at best, though San Francisco coach Jim Harbaugh must have thought it was worth a shot.

Losing a star defensive player on a 2-1 team, after all, is a lot easier than losing him from a 1-2 team. And 2-1 is where the 49ers thought they would be after a Sunday at home to get back on track following a drubbing the week before in Seattle.

They’re not, and now the questions can really begin — chief among them, whether the team that came within 5 yards of winning a Super Bowl last season has any shot of getting there again this time.

Early indications aren’t good. Dreary on defense, the 49ers are suddenly dysfunctional on offense, too. The read-option that befuddled just about every opponent last year now seems befuddling to the 49ers.

And if they don’t find a way to win in a short week Thursday night in St. Louis, there’s a real possibility the NFC West title will be out of their reach just four games into the season.

“We’re facing adversity,” Harbaugh said earlier this week. “It gives us the opportunity to stare it in the face and respond.”

The problem with playing in the NFL, though, is that response must come quickly. One-fourth of the season will be over by the time the 49ers walk off the field in St. Louis, and if they do it as a 1-3 team, they will have dug themselves a hole that will be awfully hard to climb out from.

Losing too many games presumably was on the mind of the San Francisco brain trust last week when the decision was made to play Smith despite his arrest on suspicion of drunken driving and marijuana charges two days earlier — and with plans already underway to admit him to a rehab facility. Smith had five tackles against the Colts, issued an apology and headed off to improve his life.

If Smith needed help that badly — he might have, judging from his arrest and a lawsuit that claims he fired a gun at a booze-filled 2012 party at his house — why did the 49ers wait until he played another game to get him in rehab?

The 49ers barely bothered to justify their decision, calling it a personal matter for Smith. But if the plan was to try to steal a win with Smith on the field before he went into rehab, it backfired badly in a desultory loss to the Colts.

What plans the 49ers have to bulk up a defense that has allowed 56 points in its last two games are being kept under tight wraps, too. With Smith, who set a franchise record with 19 1/2 sacks last year, out for an undetermined time and Patrick Willis troubled by a groin injury, the defense that helped propel the 49ers to the Super Bowl  last season is shaky at best.

“Football’s not easy,” Harbaugh said. “There are struggles. That’s one of the things you enjoy about the game, that there are struggles.”

If so, this could be an enjoyable season for Harbaugh and the team he is credited with rescuing from the bottom of the NFC West. After a season when everything up until the Super Bowl seemed to go right — including the decision to build around Colin Kaepernick as the future of the team — little has gone according to plan.

While Alex Smith, cast off unceremoniously by the 49ers after a concussion sidelined him, is enjoying himself as quarterback of the undefeated Kansas City Chiefs, Kaepernick has no touchdown passes and four interceptions in his last two games. His running stats are so-so, but the real issue is that defenses have found ways to stop him from getting big plays when the 49ers run the read-option that was so successful for them last year.

The NFL is all about adjustments, and defenses have adjusted. Teams are keeping Kaepernick in the pocket more, where he’s not nearly as accurate, and he has completed less than half his passes in his last two games.

“It’s more our execution than anything,” Kaepernick insisted this week.

That would be good news for San Francisco, which opened the season with a win over Green Bay in which its execution was fine. The schedule the rest of the way isn’t terribly tough, with two games against Arizona and one against Jacksonville, and the next time the 49ers play Seattle it will be at home. There’s still time to turn it around, still time to discover the magic that was last year.

It begins with a short-week game in St. Louis that is almost a must for the 49ers, who despite all their issues are still a 3-point favorite. Win it, and they can get their momentum back with plenty of time to prepare for the Houston Texans at home the next week.

Lose it, and a season that is already unraveling may be as good as done.