The relationship between reason and religion in Locke's theory of natural rights

In his Second Treatise of Government, John Locke offers rational and religious arguments for natural rights. The rational argument grants the rational individual the authority to determine the morality of actions whose morality the law of nature does not. In the religious argument, God's will determines the morality of all actions; thus, it trumps the authority of rational individuals. Reason and religion conflict concerning our duty of charity. We ought to be charitable to the poor whose poverty is due to natural defect or uncontrollable circumstances. We should not have to help those, whose poverty is due to their own neglect. However, Christianity exhorts us mercifully to help the poor regardless of the causes of one's poverty. Textual passages from Locke's works indicate that he believed God exists and that Christianity was religious truth. Thus, Locke believed the religious argument for rights more authoritative, because God's will---the will of a most wise being---is superior to human wills. Oddly enough, Locke states in his A Letter Concerning Toleration that each rational individual is "orthodox unto himself" and must determine religious truth for oneself. I argue that one may explain the relationship between these conflicting arguments in the following way. Locke believed that a genuine acceptance of Christianity was possible only in a political society in which government's purpose is to ensure that human beings respect each other's rights to determine their beliefs of the good life and to act accordingly.