Have you ever read anything written before the 20th century?
While you were reading, did the story turn you off because every single male character was "deplorable"?
It's not likely, because they were simply being normal for the time.
Yet those same normal people didn't recognize women as people, didn't allow them to vote or own property, … .
Everyone, men and women, were what we would now call misogynistic, but were at the time called normal people.
Except for those very few that wanted to change society, no author would ever have depicted these ordinary people as deplorable.
Men naturally took it for granted that they could vote and own property, and women naturally took it for granted that they couldn't.
Had their characters behaved differently, the unnatural attitude would have stuck out like a sore thumb and ruined the story.
Authors had no problem with this though, because to them this situation really was normal.
Read anything by Dickens or H.G. Wells or Defoe or Shakespeare or … .
The rare times that anything resembling "women's rights" could ever appear in their works would be if the authors intentionally put it there for a very specific purpose.
When writing, point of view is so important.
When you are writing about the 17th century, it had better sound like you are part of that time, not an observer from hundreds of years in the future.
I'd like the reader to like Nathan despite the fact that he is still a slaver.
Then don't depict him as "a slaver".
Depict him as a typical citizen of his time, doing the things typical citizens did, saying the things typical citizens said, etc.
In fact, what you want Nathan to do is actually quite illegal and anti-social.
It's going to be very difficult to get away with it (both for him and for you).
He will appear deplorable, but that's because he wants to break the laws of society, not because he follows them.
But whatever you do, know that inserting anachronistic editorial comments into a story will ruin it.