You can - at one point or another- kill every single last m******er. Exceptions to this are the games few "safe" zones, where you cannot use any weapons. Though this only applies to random NPCs, as all other mayor characters with speaking roles that are just tiny bit relevant to the story can be killed.
NOW IS THE POINT OF NO RETURN-SPOILERS FOR ONE(?) OF THE ENDINGS
At the end of the game on liberty island you are presented with three factions- the templars, the illuminati and apostlecorp, e.g. the dentons. Each of those factions wants you to upload a schematic to them, so they may shape the world in their view.
The "fourth faction" is your fellow Tarsus comrade Leo Jankowski, who suggests to f*** it and nuke 'em all to hell. At this point of the game, he is partly Omar-izised. If you then kill the templar leader Saman, the illuminati leader Dumier and JC Denton-twice, once before destroying his machine and once after, you'll get a cutscene were basically the whole planet has been wiped out with almost all of humanity after 200 years of war- only the Omar and the ones "omar-izised" will be able to live in this environment- as it is mentioned numerous times, that they are very capable of living in hazardous environments. Oh and they also seem to conquer the whole universe...
Hope that helped
EDIT: Oh, and of course NPC react to your actions- so for example if you want to kill every little schoolgirl in the Tarsus Academy in Cairo, you can do that, just don't expect no repercussions- you'll get a message n your infolink by Donna Morgan afaik.