I think it's going to go even further than this. The manipulation will be essentially part of the birth of the Patriot AI systems, or at least the idea of them. The quote about research in Africa being "bigger than Metal Gear" from the end of the 2013 Red Band trailer - I'm willing to bet we'll see how Cipher will be essentially about controlling the situation and the information surrounding it to make BB fall from grace and to change public perception of him.
So we'll see this play out with BB basically being manipulated into doing a whole load of awful things, all of which he thinks is going to lead him to his 'revenge', but all of which are making him appear like a monster to everyone.
Thus, by the end of the game, we'll still view BB as a tragic, sympathetic figure who was basically tricked (similar to how Lucas wanted everyone to see Anakin/Vader), but in the game world, BB becomes a monster. It'd be the perfect precursor to the following games where the Patriot proxies are basically pulling the strings behind the scenes all the time.
Or something. I don't know. I'm quite tired, and don't seem to be able to fully articulate this stuff today