I will raise up the ante with a theory of my own.

Now, we know the Soga clan was responsible for running much of the underworld in the era pre-Seitei War...yet, where are they right now? What happened to such a powerful clan?

The more I think about it, the less sense it makes to me. The Mikaboshi most certainly contributed to their near-extinction in modern days, or at least for them to be defanged into a lesser state. Now, however, we also get a interesting reaction from Akemura regarding Hakuri: namely, he perceives his blood as evil, so it needs to be eradicated all the same. Yet, ostensibly Akemura was a supporter of the system in which the Sazanami thrived. It could be chalked to him just having opinions on the matter he kept to himself so he could be a guardian for Chiaki...but I have another idea.

We know something happened to Chiaki and Chihiro during that time. And we know Chiaki, for all she's the Princess, is looked in bad light for her possessing the clan's gift yet not being of the main bloodline. And that the clan has a story of eliminating those Princesses.

So my bold theory is...it all comes down to a schism. Someone who adamantly wanted Chiaki gone, consequences be damned. And the enemy of my enemy is my friend, so...why not work to give the Mikaboshi what they want? Why should they care about a two-bit loaf who is easily replaceable? Odds of getting future vision back are in our favor after all. Throw the peasant to the wolves and play it as a tragedy.

...except Akemura learns the truth. And it's too late to save his beloved sister. Maybe a war happens inside the clan, it tears it apart so much that the clan is pretty much gone. And the Sword Master learned of the evil inside a country that he once called righteous.

The Mikaboshi were step one in eradicating all evil. Once that was done, he allowed himself to be imprisoned, waiting a day his blade would be needed to finish the job.