What does mean to be truly a free thinker or a thinker who is free?
Jesus said, "If you hold to my teaching, you are really my disciples. Then you will know the truth, and the truth will set you free." He also said, "I am the way and the truth and the life. No one comes to the Father except through me."
It is obvious that freedom is tied to truth - knowing the truth will set one free. Deception or deceptive thinking will cause one to be in bondage but Truth or 'truth' thinking will set one free.
Knowing the truth is more than just cognitive knowledge but it is actually knowing the very Person who embodies all truth - the Truth Himself, Jesus Christ.
So if you really want to think freely or freely think - you need to know the Truth then truly You are free to think as the Truth thinks.