Both Herod and Pilate were political appointees and the priests were the natural form of leadership for the Jews.

Therefore the priests got their way.

From a personal experience, in supreme courts I know that Judges will rule towards Banks because of their power even though substantial facts could be against those Banks.

Nothering has changed, even today. 

There are two things that come to mind.

1) Jesus would feel all his pain knowing he was innocent but knowing that the pain was a means to his ultimate end.

2) I also think of other prisoners today who are abused and killed when they are also innocent.