The final confrontation between Shepard and Kai Leng was so powerful for me not merely because he killed Thane (and Miranda in one playthrough), but because Kai Leng had taken the prestigious training of N7 and distorted it, making him a black stain on the N7 service record. It is a sentiment that only she and Anderson share and that Hackett can’t understand, because he never experienced the Interplanetary Combative Training and Rio, nor did he develop the familial bonds achieving the N7 ranks bestows upon its members.
Kai Leng isn’t just a traitor to humanity by that point. He is a fallen N7.
The fight at the Cerberus headquarters means so much more to me, because Kai Leng so infuriates Shepard simply because he lives. His taunts also hit harder, because he is trying to mock Shepard from the position of an N7, to which she retaliates in kind. (My personal head canon is that a part of the N7 crede is ‘I will return ‘Mission Successful’, or I will not return at all’).
When Shepard stabs Kai Leng, she is also rectifying a mistake on behalf of all her fellow N7’s, who are all there with her in spirit.