If I may be so presumptuous as to offer some advice, knowing as always that it is just that, and ultimately you will do what you feel is correct.
But…
If I was on the opposite end of the mail your describe, I'd ignore it.These kinds of exchanges rarely produce anything worthwhile. I speak from experience.
You've chosen to write about a topic that some people have strong… in some cases very strong feelings. There's certainly nothing wrong with that. I have read what you've posted of the story so far and there's nothing that even hints of being offensive. In fact, I'm enjoying reading it.
In some ways it's like someone writing about religion. Those stories also get strong reactions.
You can write the person back and then they may (and often do) respond still negatively, then you write back again and this might go onfor some time. You won't change the person's mind, and they won't change yours.In the end nothing is really accomplished and while you might have thought you could justify yourself, you suddenly realize that the person on the other end is unreasonable and just won't see your POV.
At the end of the day instead of justification you feel like your POV really doesn't matter to the person complaining.
I've learned to let these things sit. I chalk it up to freedom of speech and move on. It's rare to get unanimity on something especially a more controversial topic. If I myself get a genuine hate mail I don't give the person the satisfaction of even acknowledging it. I know they really don't care about my opinion and simply just want to wound, offend or insult me, and I won't give them any additional ammunition.
Maybe I'm being too strong here, or not giving the other person the benefit of engaging you within the framework of a civilized disagreement were one can agree to disagree, but if you haven't written back I say just let it lay.
You can actually be pleased that you've taken a risk and tackled a topic that has some legs and is open to different POV's. It's great to write a fluff piece that everyone likes and you always get praise... much harder to do one that some might not like or agree with.
It doesn't sound like it's hate mail to me, but if you start getting into a skunk-spraying contest it can escalate to that level.
But the natural reaction is always to respond back… if youhaven't you probably will; human curiosity being what it is. If so I'll be interested to see how it pans out. Let me know. But if you're really a strong person emotionally then set it aside.
In my opinion the best response of all is to: 1. continue the story; and, 2, work hard on making it one of the best you've written. That will show the kind of person you are and your character will shine though. It will also show the person on the other end of the complaint that you have the character of your convictions and aren't afraid to express your POV in a creative way.
If I really felt strongly against your POV then I'd write my own story with a POV coming from the other side. Have I read stories that I not only disagreed with but didn't like at all? Yes. Have I ever sent a complaint or hate mail to the author... no.
This is the internet for heaven's sakes every POV including the most bizarre and downright criminal is represented. If we complain all the time we don't produce anything useful ourselves.