It's much like the Georgian RICO case, Putin doesn't have to directly order it to be responsible. There is a whole hierarchy that has eliminated opposition to have Putin remain in charge. Whether Putin doing it, someone doing it because it would Curry favour with Putin, or someone seeing his own position at risk if that hierarchy collapses. The end result is Putin is responsible for all, and not just because of the buck stops there.
Speaking out, mutinies and marches can all be forgiven. The greatest crime as Navalny and the CEO of Yukos etc committed was to be popular. That is completely unacceptable. Too many people were listening to Prigozhin so he had to go.