And the purge of the Hieda clan... Was it because of the new Yamato deeming them as unnecessary existences too?

Hieda Akyuu has lived long enough to know enough.

Izumo, Suwa, Musashi, Kumano. She's planning to destroy everything she knows about The Yamato's dark and bloody history.

Akyuu is planning to start a war of supremacy with you and the Kirisame clan within Gensoukyou. Everything else is outside of her interests.

She's continuing the ambitions of her ancestors. To rule the Yamato and pursuing the Hieda's hatred toward the Fujiwara.