Maybe Yoda had some kind of vision that "prevented" him from chopping Vader, Palpy, and all the rest of the baddies into Dark Side Midichlorians. Maybe he had a vision that someone sometime 20 years after the events of Episode III, a young man would be reared by a long-lost Jedi Master who would die on some ominous space station to help him escape so he could eventually train with Yoda (hint hint).
Well ok we all know that Yoda may have been more powerful than Vader, Palpy, and Dooku combined...but remember, he does have a deep connection w/ the Force and may have seen the demise of any hope for the Republic had he chopped up Vader, Dooku, and Palpy into microscopic lifeforms.