The Kochen-Specker theorem shows that the results of probing the particle cannot be determined ahead of time, if the questions are not. Therefore the orientation is not determined, although the answers from the two particles will agree (quantum entanglement). Because the answers agree, and there is no communication, the answers cannot depend on the order of the questions. Therefore, unless the questions are predetermined (and the particles can acquire that information), the results are non-deterministic.
The proof does not assert that free will exists at all. A fully deterministic view of the universe could imply that both our questions about the particles and the answers to those questions are pre-ordained.
The definition of "free will" used in the proof of this theorem is simply that an outcome is "not determined" by prior conditions, and may therefore be equivalent to the possibility that the outcome is simply random. Thus, the definition of "free will" may not coincide with other definitions or intuitions about free will. Indeed, some philosophers strongly dispute the equivalence of "not determined" with the existence of free will.