We can, but the point is to choose to detach ourselves from defining our thoughts as if they define who we are as people rather than what we are brought up to be and live in (illusions and suffering).
Do we have the freedom not to give pattern to our thoughts? Do you mean, not to be caught up by our thoughts? Prisoner of our thoughts?
We have a choice in whatever we do; that is why there is Kamma, or cause in affect in everything we do and think.
For some reason, I think this is more of a Hindu point of view than Buddhist. If you're gearing towards an "essence" or something mystical behind the practice, The Buddha taught away from that. A lot of the suttas seem like riddles to me because it's repetitive.
It's hard for me to understand metaphysical talk.