I'll be curious to see whether Harbaugh learns from the experience.
The message Harbaugh tried to convey invites ridicule (see the video above for one example). It doesn't matter that Harbaugh never denied the 49ers' interest in Manning. He actually confirmed the team's interest. But in trying to qualify that interest in a manner perceived to be self-serving, Harbaugh actually turned a non-issue into an issue.
The non-issue was this: San Francisco pursued Manning this offseason.
The issue is now this: Harbaugh has compromised his credibility by speaking the way a politician would speak (former President Bill Clinton's famous line about the definition of the word "is" comes to mind).
The lesson is this: NFL head coaches have lots of control, but they cannot control the message nearly as well as a college head coach can control the message. The NFL is not a college campus. There are only 32 NFL teams and every one of them commands national coverage from lots of people who lose nothing when they criticize the head coach. Harbaugh came to the 49ers from Stanford, where he was fairly well insulated relative to now. While Harbaugh made his football schemes transfer from the college ranks, the dictatorial powers don't translate the same.
The harder Harbaugh tries to convince people they were wrong on Manning, the less credible he's going to appear.