I do believe that some people can stop thoughts for a period of time through meditation, but I don't think the fact that some people can do this means that free will exists. I think uncontrolled thoughts is a single example that demonstrates our lack of free will.

Let's say that I mastered eliminating thought through meditation. What led me to that point that I could meditate enough to cancel out these thoughts? What factors in my life convinced me that eliminating my thoughts is something that I should strive for? What gave me the discipline necessary to sit down and meditate for long enough to eliminate these thoughts.

I believe it goes back to genetics and environment.