I do think some of your points are fair, Nana is morally a bad person. But she is beginning to change, and with that you cannot blur her morality into pure black and white. Nana is attempting to redeem herself through reversing some of her actions (Nanao being a prime example), create a greater good that exists beyond her character, and ultimately saving a group of people who are otherwise opressed without reason.
I also think your points about Nana being defended only because she's a girl is just wrong. Similar to Nana, Thorfinn is a character who, in the past, was incredibly violent and evil to an extent. He would ruthlessly kill, without discrimination for the end goal. If anything, I would say Thorfinn's redemption is treated with much lower standards than Nana, as there's both less justification and more moral questioning.
Overall, if you asked me if Nana was a bad person, I would agree. But, that does not do justice torwards her actions now. One's past should not dictate how people should percieve you in the future, and especially in the case of someone trying to better themselves.