The thing is, I get the feeling that while the Cthaeh is horribly powerful in its manipulations, it is not as all knowing as Bast made it out to be.
Think about it. If it were truly omniscient and malevolent, why would it have performed any action that would have led the Fae to blockade its tree? In its very essence, that prevents it from manipulating people to accomplish the greatest malice. If it were all knowing and wanted to accomplish the greatest harm, it would act more subtly so as to never alert those around it to its true nature, thus freeing it to speak to more people and accomplish more harm. And if you know EVERYTHING that can possibly happen, it wouldn't be hard to cause extreme amounts of harm without letting people know you caused it.
So, the way I see it, there are four major possibilities:
The Cthaeh can see the future, but is not all knowing--there is a limit to how well he can know what to do and how to manipulate.
The Cthaeh is all knowing, but the nature of Rothfuss's universe is more fluid and quantum--nothing is set in stone. The Cthaeh can merely influence events to be more likely to result in the greatest harm, but not assure that it happens.
The Cthaeh is all knowing and can manipulate to assure the most harm--but it nature was known from the very beginning, perhaps before it was born, and so the Fae set out to limit it.
The Cthaeh is not malevolent, or at least not totally.
There are two other possibilities that spring to mind--the first, the Cthaeh is all knowing and can assure the future it manipulates towards, but cannot control its impulses, and tries to do the most harm as fast as possible, which allowed its nature to be known. This doesn't seem likely as its nature seems to be patient--after all, if instant gratification was its thing, wouldn't it simply enrage Kvothe to do violence to the nearest possible person?
The second--The Cthaeh is all knowing, it can assure the future it selects, and it only let its nature be known...because being trapped is part of its overarching plan that in the end causes more harm. I don't want to think about this one. I can't see any ending to the story that won't break my heart if that's true.