Since a pastor (or any human being) can't look into a person's heart to determine whether or not the person has faith in Christ as Savior, he can only go on the basis of a person's personal public confession. Since your father's personal confession indicated he was not a member of your church, the pastor could not give your father a Christian burial. In refusing to bury your father, the pastor was not saying that your father was an unbeliever. He was simply stating that he had no basis for determining this one way or the other.

Had your pastor met with your father prior to his death and heard his confession of faith in Christ as Savior, he could then have given your father a Christian burial, even though he was not a member of the church. With a good conscience your pastor could have assured people that he heard your father's confession and on that basis could say he was now in heaven.

Although it is possible for someone to believe in Christ as Savior and yet not join or attend a church, it is more common for Christians to join together with other Christians for worship and spiritual encouragement. They will want to hear and study God's Word and enjoy fellowship with their fellow Christians. Unfortunately your father, for one reason or another, did not understand and practice this.