They tried to genocide his entire kingdom! It's completely justified!
I don't understand how your fucking mind works that you think Eren was justified, but Rimuru isn't. That Eren can genocide 80% of the planet, the civilians, the children, everyone, even of countries that aren't his enemies, on fears of a hypothetical future retaliation. But Rimuru isn't allowed to destroy an army that is actively trying to murder his people, and punish the 3 people in charge of that attack.
It's like something in your brain is wired wrong.
It sucks that the 3 that were spared were the 3 most responsible for all those deaths.
Been playing RPGs all my life. Never play a human when there's an option not to. This shit's old hat to me.