There is no entire machine of Judaism, Islam, or Buddism for that matter.
Actions committed by someone in one Islamic sect will be condemned by another, and so on.
There's no meaningful culpability of a group that has no way of knowing what another group does, has no way of taking action if they do know, and don't support negative actions when they become aware of them.
Holding "Orthodox Judaism" responsible for abuses in some sects would be like holding all pet food makers responsible for tainted pet food made in China. They can be categorized together, but there's no logical reason to spread responsibility beyond actually transgressors.