Was this really a moral dillema though? Like, I'm not sure the point is like "killing is baaaad" or whatever, but maybe to show just how batshit insane Momos are, sure the dude was objectively evil and deserves to die, but like Shiki said he was just a normal student not long ago, killing won't be easy for him, but now he's finally understanding that killing is the only choice, because there's no arguing with Momos, that vast majority has to be killed, that "good" Momos like his future husband are the outliers and the rest is pure evil.
I guess the point isn't if killing is bad or not, but that Shiki is scared what will be of himself after crossing this line, people love to talk about how evil characters deserve to die or worse and whine when protagonists hesitate, but let's be real here, an actual healthy, normal, sane person will hesitate to kill, even if they know it has to be done.
Shiki has no issues with Momos being killed, he's just scared of finally having blood in his hand and all that comes with it.
This isn't a moral dillema, but a personal dillema.