49ers coach Jim Harbaugh putting his ego ahead of what’s best for team

Getty Images File PhotoJim Harbaugh has been starting green QB Colin Kaepernick despite Alex Smith being healthy and ready to play.

Getty Images File PhotoJim Harbaugh has been starting green QB Colin Kaepernick despite Alex Smith being healthy and ready to play.

Will the 49ers run for the Super Bowl be aborted because of coach Jim Harbaugh’s ego? It will be if he continues to start young quarterback Colin Kaepernick.

When Alex Smith was medically cleared to play before the game against the New Orleans Saints, Harbaugh said he was sticking with the “hot hand,” because Kaepernick had an outstanding game in the Monday night defeat of the Chicago Bears.

That hand has cooled considerably in the last three weeks. Playing against three straight sub-.500 teams, the 49ers have struggled to win two games and lost the third in overtime. The problem has been an offense that has struggled to score points.

Against the Saints, a team that gave up 52 points to the New York Giants last Sunday, the 49ers managed just two offensive touchdowns but won because the defense scored two touchdowns on interceptions.

Against the Rams, a team that gave up 59 points to the New England Patriots in their game in London, the offense scored one touchdown early and couldn’t score another. Because the defense didn’t give up a touchdown, they still would have won in regulation except that Kaepernick gave the Rams eight points. The first two came on a safety on a play that started on the San Francisco 17-yard line. Kaepernick retreated into the end zone and then threw a pass out of bounds before he could be tackled, which was still ruled a safety by officials. Then, on an ill-advised call with the Niners backed up again in their own territory, he pitched the ball out wildly. It was picked up by the Rams and run into the end zone.

Against the Miami Dolphins on Sunday, the 20th-ranked defense in the league, they couldn’t score a touchdown in the first half. Early in the second half, they got a gift when an Andy Lee punt was fumbled, with the 49ers recovering on the Miami 9. They punched the ball into the end zone. Still, they had only a touchdown lead with slightly more than two minutes to go before Kaepernick faked a handoff and ran around the left side, where no Dolphin defenders were in sight, and went 50 yards for a touchdown.

That didn’t stop me from thinking, “If they play this way the next two weeks, they’ll lose by at least two touchdowns to the Patriots and Seahawks.”

Both games are on the road, on opposite sides of the continent. The Patriots are at their peak, with a seven-game winning streak. The Seahawks’ last game: 58-0 over the Arizona Cardinals. They’re undefeated at home. The 49ers had to call three timeouts last week because Kaepernick couldn’t call the plays fast enough. What will he do in Seattle, in the noisiest stadium in the league?

There is little doubt the 49ers would have won the last three games easily with Smith at quarterback. But Harbaugh wants to prove he was smarter than anybody when he convinced Trent Baalke to trade up to get Kaepernick in the second round in 2011.

Is he so determined to prove he was right that he’ll risk the 49ers’ chances at the Super Bowl? We’ll soon find out.

Glenn Dickey has been covering Bay Area sports since 1963 and also writes on www.GlennDickey.com. Email him at glenndickey36@gmail.com.

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