Thought is not the enemy. It is what we think that is the enemy. We are all conditioned with thoughts that are not our own, thoughts based on fear and past trauma. When thoughts are refined by the search for truth, peace happens, relaxation happens, a quiet mind without conflict happens.
The ego remains but it is in the background, a tool to be used by Self as needed. David Hawkins says that you treat the ego like a friendly pet. It doesn't rule the house, and it is also not the enemy when it knows its place.