I kinda want to go with the Goats Re-Reading Seacats theory (instead of what’s shown in the Confession chapter) and I believe that Sayo was the one who killed Natsuhi and Krauss, since they were her accomplices, and as she was leaving the house, George spotted her, leading to where she pretends to be Shannon for his sake (and then kills him).
Because like you said, there’s no good reason for Eva to kill them even with paranoia (even the magic narrative doesn’t have Eva/EVA having any real resentment towards Krauss when he’s killed, and with Eva’s backstory and hatred for Krauss getting the headship just for being older and a man, you would think his corpse would get played with in the fantasy narrative. Seriously, Tea Party EP2 Beato is much more cruel to Krauss than EVA is when she kills him).
So, EP3 has two killers, according to this theory: Eva, who’s paranoid, and Sayo, who wants to do it according to the epitaph (since she doesn’t find out somebody had solved it until the door message). Based on this, Sayo’s killings are: the First Twilight, staking Rudolf, Kyrie, and Hideyoshi, Natsuhi and Krauss, George, and Nanjo. (Possibly Maria, since in the magic narrative, Maria’s death is seen as a merciful killing and why would Eva give Maria a merciful death). Then Eva has the rest of the deaths: Rosa, possibly Maria (but I’m leaning more towards Sayo mercy killing her after Eva accidentally kills Rosa and runs off out of fear and Sayo feeling sorry that her roulette chose her dearest accomplice), being a cause for the Hidyoshi/Rudolf/Kyrie death (and maybe having killed one of them after one of them shot her husband?), Jessica and “Kanon”, and then Battler.
It’s really no wonder Eva went off the deep end, how Eva even was deemed capable of raising Ange after that is a surprise (then again, Japan with its MENTAL ILLNESS THAT DOESN’T EXIST YOU SILLY GO CONTRIBUTE TO SOCIETY YOU USELESS PERSON mentality, they probably were like eh, go ahead, raise her).