Bhaute, is it possible that Bhattarai wasn't calling the shots, at least in regards to the religious protocols? Could it be that other leaders in Maoist party did those atrocities and are again raising the question to Baburam?
As a second in command, Baburam should have done something about things that he doesn't approve, so he is clearly not innocent; but I highly doubt he was the one giving the command to attack people and disrupt said rituals.