Mammele,
1. Actually the appeals court said that they do not know if Silver would have been convicted under the SCOTUS rules.
2. It does not mean that he did not commit the murder. It just means that so much time has passed that it is not possible to re-try him.
3. Your contention about pidyon shevuim is incorrect. For example, Rabbi Tarfon refused to help Jews suspected of murder. According to Rashi he only suspected them of guilt. Tosafot and Maharshal disagree but also say that if he had known that they were guilty he would not have been allowed to save them. According to Rabbi Saul Berman (Boundaries of Loyalty: Testimony against Fellow Jews in Non-Jewish Courts p. 221 – available online as a Google book) Rav Soloveichik ruled that once someone has been properly charged, convicted and sentenced by an American court there is no mitzva of p”s harsh prison conditions notwithstanding.