Lets say Shisui used KA on Itachi to make him so determined to protect the village at any cost? He said he tried to use it to stop the coup d'etat, but danzo took his eye that might have left him with only one possibility to use Itachi. He wouldn't risk it if Itachi chose the to stay with the clan. Danzo represents 2 possibilities to him here:

It could also be that Danzo did it, but I doubt he would get the eye and be able to use it in such short time.

Anyway the whole point of this is to discuss "the one who knows everything". I have been of the belief that it is Uchiha Shisui, though it doesn't really matter. The person (or persons) will tell Sasuke this, and what would he then do? Would it make him change his mind to help Naruto? Or will it make things worse?

I think it would make him change his mind about it, but who knows.

Well all in all I don't see it as a high possibility, but it would be very much like Kishi to do something that would be very unpredictable, like he has been doing over and over lately.