Then get rid of the peasants?
I just did it a couple of days ago, and it worked fine for me the first time. What I did specifically was occupy Tokyo, wait for someone to start sieging it back so the sponsored rebels don't walk off, sponsored lots of patriots, and waited three years (signed peace in the meanwhile).
If you've already reduced all of them to OPMs, you probably don't even need to take steps to prevent the patriots form walking away; just occupy Tokyo, sponsor lots of patriots, then sign peace.
I got the achievement, six months after I was supposed to! Yay!
I had the same bug a lot of folks were having, you occupy all provinces and then you get a million messages (really, one per day) saying the Shogunate was disabled, when in reality they weren't.
I let the spam messages go for a year, and it turns out that eventually the shogunate were disbanded! Oh, the joy!
Thanks for your help, qoou (even though it did not work for myself, haha).
Back to the "RAAGIN"ing!