As of right now, it seems the only real "warcrime" you can commit is a saturation bombardment. What about adding some more?
Ideas:
Instead of capturing crew alive, always have an option to harvest their organs instead, this applies to salvaged crew and officers as well as post battle crew. I think this would also add a nice source of harvested organs which in my opinion is one of the more underutilized trade goods.
Under the same vein, what about a building besides the cryosanctum that harvests organs? Like in Rimworld where you can get an entire operation going. It might even increase the stability of the world if it's treated as a blacksite sort of situation.
Under the same vein of increasing planetary government type warcrimes, what about adding a special action for deleting a luddic path cell from your worlds permanently with a mass execution, or a buildable surveillance type structure or some kind of police HQ thingy. I would definitely like to see another way to manage a colony which instead of going for the current free market approach, instead is more authoritarian/command economy. Maybe this would give factions like the Sindrian Diktat and Hegemony some more unique flavor.
And lastly, IMO it would make more sense if things like space colonies like Kanta's den and such were not destroyed by a saturation bombardment, but instead by landing marines and manually killing everything that moves. It seems kind of weird to "drop" fuel onto an orbital habitat after all.