I think it's actually really important for the story that the Shokoku Islanders were the instigators in this conflict.
Akemura's actions aren't evil because the Shokokers were completely innocent in this conflict. They're evil because even if the leadership attacked Japan with no mercy and even if they were so powerful and brutal that it made creating the Enchanted Blades necessary it still wouldn't justify the complete eradication of a civilian population. Collective punishment is always bad, no matter the reasons that were used to justify it.
Remember what Akemura said about Hakuri, that he deserved to die because he was raised by the Sazanami's and had inherited their sorcery. The Sazanami clan was evil, they took part in human trafficking and were left alone by the Kamunabi because they had too much power and influence. Chihiro and Hiyuki killing Kyora, any Sazanami's that got in their way and destroying the Rakuzaichi along with the rest of the Sazanami's power base wasn't wrong. That still doesn't mean Hakuri would deserve to die, even if he hadn't helped them.
I think it ultimately makes a more powerful message if we are made to see the Shokoku Islanders as not innocent victims, but active participants in the conflict. The Malediction isn't evil because the Shokoku Islanders were innocent in the conflict, it's evil because genocide is always evil, and I think it's pretty safe to say that's the direction Hokazono is going with.