Hi April, Hmm, this situation is certainly causing you a lot of anxiety and uncertainty, even though it seems clear your motives and intentions are completely above board and honorable in the best possible way. I have never published a book but it does sound to me like some of the kinds of concerns you raise are ones your editor should be able to help you with. Have you discussed this with her/him?
Also, it appears from what you say that essentially only one person has raised concerns about your respectfulness towards your 6th great grandfather, whereas the rest have been entirely positive. Obviously many books are published about real people, most of which are by no means entirely positive. As you point out, 'real' people are never perfect but struggle with the realities they face and do the best they can. To do so is the best any human being can hope to do. And you seem to be attempting to portray 'John' in exactly that realistically loving way. How is that "being disrespectful"?
What is this relative's relationship to you and why is their opinion causing you so much anguish? Why does he/she need to protect 'John', whom they never knew, in this manner? These are questions you don't need to answer here but only in your owe mind.
And BTW when I mentioned 'superstition' in my earlier response I was referring to a personal response I have to people who are, in my opinion, unduly concerned with protecting the reputation of a deceased person, even if it violates or distorts the truth. The whole notion that one must not "speak ill of the dead" seems to me to violate the concept of speaking truth. What 'truth' are they actually concerned with?
It does not seem to me that you are being disrespectful at all but rather that you are honoring 'John' by giving him a voice as you are able to reconstruct it. How wonderful that you have personal letters and documents that actually give you exceptional access to some of the inner reality of a man who lived through tempestuous historical times! It sounds to me that you have almost a duty to share this with the world!
Another idea is that there are a few others in this thread who have actually written and even published books like yours. You might want to start by reading what they have posted here.
So do speak to your editor about procedural and/or legal concerns. And if necessary, consider trying to find someone independent such as a counselor or clergy person who can help you sort out the more personal issues. Five years is a considerable part of your life; do not let one person dissuade you from an entirely honorable and potentially historically significant endeavor.
Best of luck April! I for one want to read this book!