Focus on religious aspect:
* Secularist: Someone who believes in separating religion from government and public life.
* Atheist: Someone who doesn't believe in God.
* Agnostic: Someone who believes that the existence of God is unknown or unknowable.
* Non-believer: Someone who does not share the religious beliefs of the missionary.
Focus on the purpose:
* Exploiter: Someone who takes advantage of others for personal gain.
* Colonizer: Someone who seeks to establish control over a foreign territory.
* Proselytizer: Someone who seeks to convert others to their own religion or cause (can be a negative term).
Focus on the method:
* Diplomat: Someone who uses tact and diplomacy to achieve goals.
* Humanitarian: Someone who works to improve the lives of others.
* Social worker: Someone who provides social services to those in need.
The best antonym will depend on the specific context in which you are using the word "missionary".