Meaning of the phrase "the wrong side of history"

Being on the wrong side of history means that history will judge him as the person who was "in the wrong." For instance Ghaddafi will be judged by history as "in the wrong" for bombing his own people.

The phrase refers to someone who supports (or supported) a person, country, movement, etc. that when viewed from far enough in the future that it's considered "history" was considered to be the "wrong" or "losing" side, even though it may not have been clear that it was the "wrong" side at the time.

For example, former US Senator Strom Thurmond was heavily opposed to the civil rights movement in the United States and was pro-segregation, etc. At the time, it wasn't especially clear which way the civil rights movement would end up, nor was it as cut and dry a moral issue as it is considered now. In the view of history, however, it's clear he was on the wrong side. (And I should note that he admitted as such later in his career)

In the case of Gaddafi, it means that his government will lose out and in the long run, it will be considered the "wrong side" of the conflict.

In practical use, the phrase is used when someone wants to characterize their opponent's position as old-fashioned or out-of-date. When used, it is asserting the idea that in the future the vast majority of people will look back and view the position as wrong.