To me this always has been part of the story to show that there's no real good or bad side and pretty much everyone could have a skeleton in their closet. We see the story from the perspective of the settlers, but that doesn't make them the only good people (and the British the only bad ones).
In the movie (at least the higher ranks of) British soldiers are typically depicted as egoistic and (some of them) as cold-blooded murderers. Benjamin on the other side is just a loving father who joins the battle seeking revenge and to end the whole thing.
Except he's not, and he probably did similar things in the past, which is hinted at by the whole Fort Wilderness storytelling (as far as it happens). He just doesn't want to remember or talk about it, because he's now fighting people that are quite like the person he (most likely) has been in the past.
From what I know, there were conflicts between settlers (British and French) as well as native americans. However, the whole event (as well as the movie's main plot) are made up and only loosely inspired by actual events.
A quick google lead me to this article explaining several facts (and fictions) surrounding the whole Fort Wilderness plot. In short: Some things like that happened, but the actual location names are made up. In these conflicts the British settlers (so Benjamin most likely as well) were those burning down houses, murdering families, etc.