I think that Mr. Roddenberry demonstrated naivete when it came to the issue we are discussing. Human beings, regardless of how advanced they are, will need to protect what is theirs from others, and that is the purpose of a military. I believe that Mr. Roddenberry had the right to be called the creator of this franchise, but it was the work of others who made it possible for the franchise to be both believable and sustainable. When Mr. Roddenberry exerted his influence, as happened in TNG, he created unrealistic hurdles that hurt the storytelling potential of the franchise.
I think that TOS is no more contradictory than what has happened historically. The British Empire would send out captains to explore uncharted regions of the globe, and, when a call to arms was announced, that these same captains would answer their empire's calling and defend the empire. As an example, there is Captain James Cook who saw action in the Seven Years War and would later chart the Pacific.