Alt does not longer exist (she "died" in 2013).
It's a true AI who use Alt datas.So "innocent/pity/empathy" do not probably mean anything now (it's just other obstacles that she take care...).
And anyway about murdering "innocent peoples", Saburo did it too, Corpos did and do it too, Johnny also did it too...
(And engrams, as Johnny said : "what they could expect better ?". So they are not longer "prisoner" in Mikoshi)
Edit : But she help Netwatch to build the Black Wall to protect humanity... So not black, not white, but as always, greyish
Basically as
@CS554 said, she lives in a plane of existence that "humans" will probably never be able to understand (can a goldfish understand a man...)