Well normally I wouldn't appreciate that, but I think it was a vital addition to the movie. We identified with him, and felt most of his emotions as he went through his personal journey.
Many of the actions attributed to the doctor did take place, but were done by various people. He was basically a combination of characters:
For example Idi Amin's wife did have an affair with his physician. When she tried to have an abortion, she died because of complications in the village. When Idi found out, he had her corpse hacked into pieces like the movie shows. However the movie mischievously skirts the scene where she died because of medical problems, and just cuts to where the Scottish doctor comes across her gruesome remains.
While we naturally assume that Amin had her tortured alive, that's not what happened. And if you think about it, the movie is very clever in that it skips the scene and lets us naturally attribute it to the man's monstrosity. So while he did murder a lot of people, his wife wasn't one of them.
Later when the movie depicts Dr. Gariggon being tortured for attempting to poison Amin, there is some truth to it. Amin actually had the physician who had slept with his wife tortured and murdered.