That is the problem with the Bene Gesserit; their consuming need to control everything and everyone. You'd think they would have realised that their 'control' was just an illusion when Jessica disobeyed them. If they can't keep one sister from independent action how could they ever hope to control the Kwitzach Haderach? They were fooling themselves the entire time. The illusion of control is a recurring theme throughout the Dune Chronicles.
The Baron was under the impression that he was more powerful than he really was. The fact was that without the secret aid of the Emperor's Sardaukar his forces never stood a chance against the Atreides.
The Baron was just another pawn/cog in the great political machine of the empire.
Ironic , the people of that empire overthrew machine rule only to end up slaves to a political and economic machine of their own making.