Rule # 3: Keep Your Conscience Clean. If your characters are based on real people and you are using the names, be reasonably responsible to the originals. You are probably going to have to fill in a lot of gaps in the historical record: you may know from the record what a person did and when he did it, but not why. It's the "why" that defines his character. Ask yourself: Am I getting this right? Am I getting it close to right? Am I doing this person a disservice?
Rule #4: Resist Judging Your Characters. We live in the 21st century with certain shared values: our society disapproves of prejudice and chauvinism and provincialism. But your characters are people of their own times; allow them to be bigoted or politically backwards. Don't pass judgment on them, don't apologize for their mistakes, and don't attempt to make them all into free thinkers who are ahead of their times. You have to be able to see the story from their perspective, even if it offends you. If you judge your characters, you will date your book. Years from now when your own moral sensibilities are antiquated, your book will be too.
CPS: Some important points here. I run into these very issues in my upcoming book, "The Road to Frogmore." I'm writing about real people -- abolitionists -- who are dedicated to emancipation for slaves but constantly facing their own critical attitudes toward those slaves. Are they prejudiced? My 21st-century sensibilities say they were, but they don't seem to realize the depth or significance of their reactions. So how to treat it? I'm still wondering if I got it right.