First of all it is not at all clear that the person mentioned in the Gemara that some meforshim understand as a reference to Jesus, is actually talking about the same person that Christians worship. The details of his life as described in the Gemara are widely off that of the Gospels, such that the Yeshu of the Gemara lived nearly 100 years earlier. There is a good chance that they are not the same person and it is a mistake to attribute the activities of one to the other.
Second of all, the “Sanhedrin” that condemned him to death was not the real Sanhedrin (which had already moved to Yavne 50 years before the destruction of Bais Sheini). It was a Tzeduki Sanhedrin (i.e. made up of apikorsim) that had no halachic legitimacy at all (and probably were just doing what they thought the Romans wanted).