1) Overall I sided with Amita. Although for the first choice mission I sided with Sabaal because I thought that people lives are more important than some intel that we know nothing about and may or may not be important. After getting to know Sabaal better, I wanted nothing to do with him anymore and sided wit Amita for the rest of the game. Progress > Traditions that objectify little girls
2) I heard Noore out. While the things she did were horrible, she did it for the family. I mean, think about the things Ajay did just to fulfill his mother's last wishes. Is he any better than Noore?
3) I let Pagan live. Honestly, I was so fed up with Golden Path and their bullshit that every moment I got to talk with Pagan was a bliss. He's awesome.
EDIT: Just killed Amita as well. As expected she went mad with power and I had to put her down. Really love the fact that the game actually lets you do that