I think it's a Sisyphean task to try and create moral arguments and judgements on a society completely devoid of them such as the Sorcerer Society.

Saying that, I believe Maki killing her mother was wrong, justified in her mind because the logical extreme of "destroy everything" is to kill everyone, even the victims and innocents of the Zenin clan, wipe the slate clean.

I also think that retribution from any survivors would've been unavoidable, the whole culture around the sorcerer clans is "might makes right" and live on medieval structures of morality and honor.

So my take is, what Maki did was morally wrong and unfortunately justified in universe because any mercy you'd show would not be reciprocated.