Remember, the Pats received penalties for what the league deemed as illegally taping opponent's signals on the sideline in 2007.
Clearly, the consequences the team endured were based on practices after the team won three Super Bowls in four years from 2002 to 2005.
Harbaugh's statement was most likely regarding the fact that the team did turn over tapes from regular-season games from 2000 to 2002, including the 2002 AFC Championship Game against the Pittsburgh Steelers.
In fact, Steelers chairman Dan Rooney said the following about the title game taping to the New York Times: "We consider the tapes of our coaching staff during our games against the New England Patriots to be a nonissue."
Because of that, Harbaugh didn't need to say anything about the legitimacy of New England's titles. It was never proven that their somewhat sneaky practice gave them a direct and illegal competitive advantage.
Anything he planned on saying about the "stain" next to their championships was bound to be purely speculative.
To think that videotaping of coaches' signs was the reason the Patriots were able to advance to and win three Super Bowls in the early 2000s is a bit far fetched.
Harbaugh should have just left the issue alone.