I'm on the fence about the "are old battle thralls turned into fallow slaves" question. I think it's possible to let them stay free, as long as a few Ur-Quan or trusted thralls are around to keep things under control. To save effort and quote myself:
Quote from: Me, in another thread somewhere.
It seems that fear of the Ur-Quan keeps things working pretty smoothly most of the time - but if they not around then things fall apart pretty quickly.
Perhaps in other parts of the galaxy where races have been under the Ur-Quan for hundreds or thousands of years, there are trustworthy thralls who can keep matters under control in the absence of their masters. But in this neck of the woods, the thralls have only been conquered for a few decades, not nearly enough time to develop any sort of relationship other than one based on fear of annigilation.
Such favoured thralls would have an interest in maintaining the Hierarchy system, and perhaps only a few Ur-Quan would be required to keep an eye on things.
As for the Doctrinal Conflict: In a way it was not a fair contest, as the Kzer-Za were not allowed to use The Path of Now and Forever to it's full extent. They've been enslaving races for thousands of years, but when it comes to the crunch, for some stupid reason of honour, or tradition, they can't use their huge empire to their advantage.
It doesn't make sense to leave Dreadnoughts behind in conquered areas, since those are the only ships that can be used for the doctrinal conflict.
Which I think is stupid, as outlined above. Imagine the difference that a few Terminators, or Eluders, would have made in the Doctrinal conflict. I guess you could argue that this does suggest that all the former battle thralls were eventually slave shielded, but I'm not entirely convinced.