I don't want to seem mean, but...if I had to sum up that episode in a single word, it would be "misconceived". And if I got a bonus word, it would be "woefully".
The problem isn't the bad history. I mean, that's a problem too, especially as the script goes out of its way to draw attention to it--when one character spends half the episode deeply concerned with the possible rise of Napoleon to power, having him end the episode surprised to hear that a Corsican soldier might someday take the throne of France is probably a mistake. But the problem isn't even that the story is set in 1794 when Bonaparte isn't a significant political force in France and he wouldn't be offered power by Barrass or opposed by Stirling. To be honest, if they'd gotten the history right, the episode would have been even worse.
Because the meeting is the climax of the story, such as it is. Ian's been looking for Stirling since Part Two, Stirling apparently has one last vital task he needs to complete before he can leave for England and the others need to risk their lives to help him because Susan's been effectively written out of the story but is at least important as a MacGuffin, and the grand and vital task is...finding out something that the audience already knows. Or would, if they'd gotten the history right. (Maybe that's why they picked Napoleon--it probably would have been a less dramatic scene if Barrass had met with about a dozen or so guys that nobody remembers and agreed to form the Directory, a combined group of influential politicians who would then set up a provisional government and ratify a Constitution to...)
Ultimately, this is a lesson learned for Spooner. As much as he tried to subscribe to the Lucarotti philosophy of the historical story, to the point of setting the final scene inside the TARDIS so that everyone can speculate about why they couldn't change the history of France even if they tried, he's really more comfortable with the action-adventure model of story. And in an adventure, the hero has to have consequences to failure, because the structure of the adventure story makes us aware that they're pretty much immune to danger themselves. Nothing anyone did had consequences in this story, not for themselves or anyone else, and Spooner had to be aware of how hard that made it to write as an effective piece of drama. In order for him to be able to function as a writer and later a script editor, everything the series has tried up until now has to go. And with the next season of stories...it pretty much will.