In studying the laws of דינא דמלכותא, I heard a shiur from R’ Schachter. In one of his comments he stated that if the law of the land meted out a form of judgement that far exceeded the expected outcome of a prosecution under a formal פסק דין from a סנהדרין, this implied a situation where there is a clear conflict between Torah Law and the Law of the Land, and creates Halachic tension.
We are limited in what we can do in such a situation since we live under שלומה של מלכות and, in the main, are very appreciative of the system of laws enacted, even if they aren’t completely motivated by satisfying the requirements of the דין of a בן נח.
Accordingly, in this case, based on what I have read, there may have been a miscarriage of justice in that (amongst other things) the presiding Judge exercised irregular behaviour. This would then imply a new court case after which, presumably, justice would take its course. Given that Rubashkin is widely known as an איש צדקה it seems to me that his efforts for a new trial should be supported in any way that people are able: either through דורון or תפילה.
In summary: until the judicial process is fully exhausted, he is the proverbial חצי עבד וחצי בן חורין in my eyes. There is a ספק and in the case of a ספק we help someone seek a just outcome. At the end of the day, he may well be found guilty in a new trial, or may receive a lesser/larger sentence, or may get off on a technicality. Que Sera Sera.
Until and if that happens, those who are uncomfortable with supporting the effort—and I understand their viewpoint—should simply adopt שתיקה. There is no חיוב to protest against your fellow Jew until the process has ended and something else unfolds.