(SPOILER)That we don't see her thank the soldiers doesn't mean she didn't.
And no, the idea of dying alone with electronics around you is sad, and that was pretty touching, but nothing that would make me go "woah", or even begin to assume that this automaton somehow grew a soul. There is nothing in this game's universe that suggests even a slight possibility that a machine can somehow grow a soul. There is no foundation to believe such a thing could even happen. And yet people suddenly treat it like it's a person for some reason?
And believe me, I say this as a person who think that machines IRL could some day possibly have souls. There's just nothing in the story to really warrant the reaction from the characters that they had.
To me, the story came across as kind of wasted potential, especially after so many people said (not just here) that it's so sad and dark. I just think it's pretty dumb that 1) they decided that a robot still supplying soup to a dead guy is a good reason to prohibit entry to that area without telling anyone why and 2) I feel bad for the thing and I think it's way sadder that they really think it's the righteous thing to just have it repeat this meaningless activity for eternity instead of trying to actually put it to good use so that it can have a new purpose instead of constantly living in a delusion.
The most frustrating thing here is that there is an interesting story buried undreneath. Everyone says that the whole historic even we witnessed is lost to history - we never find out why or how, and it goes nowhere aside from "oh there was actually an old guy there that died and his robot thinks he's not dead yet." And it really could have gone somewhere dark since the lack of historical records is just asking form them to repeat mistakes from the past, which again is flirted with briefly but is quickly forgotten.
So yeah, this story could have just been handled better. Heck, i think the whole scenario would have worked much better with a very simple change - just let us visit the shack and see the robot in action ourselves, without adding that pointless story in the present that goes nowhere. I think it would have been much more effective then.