Rather than multiple measures of relation, which certainly have merit, i'm not arguing against, but would it not be simpler to just have enough headroom in the range of possible relations to allow a huge diplomatic hit from ship loss?
A set back worth years, if not decades of diplomatic effort. If you have enough goodwill stacked up, perhaps not war, but definitely not the trust you had.
Across all of history there have been examples of different peoples meeting for the first time, unable to effectively communicate for language barriers and differing cultural norms, some have come to start war, some have started war without meaning to. Lets set that aside and worry about those that managed extended peace before war broke out.
Granted, potentially very different alien species may not even realise their opposite is even looking at them if they cannot see what they recognise as a face, or even just eyes, or possibly even that they are trying to communicate at all, those early days are fraught with challenges, miscommunication and misunderstandings. War should be easy to get into, and hard to get out of during this period.
Given enough time though, you learn to communicate with them, their culture, ideals, how not to offend, and what they view as a form of apology. Any less and one must ask what those diplomatic envoys have been up to all those years, getting paid to chat and socialise, formally or otherwise.
That knowledge and trust could lead them to understand, for example, that rogue elements have attacked them, it was not sanctioned, the aggressors have been neutralised, and the host nation seeks to make amends. Tense situation, but if the diplomats have done their jobs well, it doesn't get worse.
More likely, it could lead to understanding of an accident. We didn't fire at you, we didn't even know your ship was there, we couldn't see it on sensors. Alas, our missile had an active sensor aboard and when its original target died it was able to see your ship and engaged it with unfortunate results.
As far as having the AI discern a degree of player/AI intent without much effort, perhaps a pair of fields in the active missile/salvo object and relayed to any child objects spawned via stages, referencing the original target the firecontrol was set to, and the originating launch platform. If the ship hit by the missile, was the FC target, be upset, that was intentional. If the FC target was another empire's vessel, most likely an accident, be less upset. If the target was a waypoint, don't be quite as mad as if you were the target, you might not have been, but it might not have been an accident. If the missile also sets itself as launch platform when it is used as a mine, then that can be factored as well, since mines are less than an intentional strike, but more than an accidental blow.
Extend that intent to loss of a ship, since a single salvo acting as one entity of many may accidentally smash a target other than intended, coupled with enough headroom that accidental loss of ship plus maximum/near maximum relations results not in war but badly damaged relations. Two ships should be nearly, if not impossible to afford the penalty without war within a few years/decades of each other.
As a modifier, large powerful salvos will still be more harm than lesser ones, so bigger ships would, assuming only the damage received is counted rather than delivered, by default convey larger penalties with or without any modifier, so you perhaps could never hit their battleship hard enough to kill without triggering war, but a scout ship, a tanker, or some other fragile vessel, quite possibly.
