To be fair we don't really know. Primals do temper people, we've seen that. How that works with Primals on the scale of Hydaelyn/Zodiark or whether the free will we think we have is even free will is completely unknown.

There's a lot unanswered with Emet too. He's very likely telling the truth but he isn't telling us the whole story. He claims his race was "perfect", yet the cataclysm that endangered his world didn't just materialize out of thin air. Something caused it. Their race was messing around a lot with creation. Also why did some of his people feel that threatened by Zodiark? We already know Zodiark required sacrifices to maintain "peace". Emet very likely didn't give us the whole picture. Perhaps, being tempered by Zodiark, he couldn't give us the whole picture in the same way a beast tribe tempered by their primal would never question it.

I imagine there will be many more surprises to come, we've only started the expansion.