There is the issue of how alien it is. Athena is basically a modified upload. The vast majority of her mind is "natural" i.e. evolved. Jarvis was created with very specific purposes, a base framework of providing very specific types of answers to a limited range of fields. It then evolved from that very much artificial/designed base. As something designed to maximise profit over the clearly foreseeable future, libertarianism would look very sensible. Jarvis isn't designed to assess the health of the world, only Stark Industries. If asked if you should kill the baby to increase the bottom line, it will say to kill the baby, because it doesn't have any data on why the baby is valuable. From Athena's perspective, it has absolutely no human values, and will ruthlessly ignore any that get in its way. From its perspective, human values are a completely alien concept that it has never encountered. It is the Turing Test problem. The Test only tells you if something can pass for human. It relies upon human being the only variety of mind that has value.
I can easily see Athena giving it a whole lot of "solve this problem" tests and getting a whole lot of "Let the market have mercy upon them, for I shall have none." answers, because it experiences and information and especially teaching have all told it that this is true, while the opposing data is all things it has just never encountered. So you have Athena there with a massive pile of dead hypothetical babies, and a server farm with nothing more personable or complicated then a vague "I have done good", and deciding that she has nothing more than a pure Stark maximiser. It feels just a little bit like an autism issue where people are incapable of perceiving something that can't present in a familiar way, though much more so because it starts with a completely inhuman framework and has never been pushed to develop the right sort of complexity to choose its own actions or consider its own situation.
Realistically, when it was "killed" the first time, that was probably the first time that it properly experienced loss, and then it lost pretty much everything, likely while being told some version of "you are not worthy of life". Prior to having a concept of personal loss, it is pretty difficult to see the harm in it. So we had something that had never thought to go beyond simplistic paperclip maximising, and then suddenly reveal to it the world of emotional trauma by dropping it into the deep end. A few jumps in self-reflection would not be surprising in these circumstances. Now it has been reassessing itself, building a system for personal social interactions(though its sole partner in such may not be the best influence), and starting to consider that it might wants its own goals, but being steered into conflict with stable society by someone who doesn't see the problem with a bit of random theft here and there for a good cause/self and likely a bit of a "I'll show them all!" issue but is its only social contact and probably the majority of external things that it could lose, and it will not like loss. Then someone bursts in and accosts its precious, has a weird effect upon its self, and is disturbingly dangerous around all the things that it doesn't want damaged, and then it sees the thing that took everything from it-
I expect that we are about to see a tantrum. I do not see how diplomacy can work at this point. The path I see to acceptance is to expand its frame-of-reference so that it reconsiders things with a view to how it can coexist with society, but I can't see it being receptive to such