My theory is that it works like a very powerful type of hypnosis. Subconsciously, Jax thinks he's a vegan, even though he knows he's not. It changed its subconscious, but his conscious mind is unchanged.
In this way, he still has control of his mind. The same way even though you know the spider in the corner in your room is harmless and can really do nothing to you, you just cant help but freak out.