Oh I see. I thought you meant a circular argument, as in "The bible is the word of god because it says so." What you say about Trek though, is a very big part of why I love it so much. I think there's a lot of Star Trek in me. It had an enormous impact on who I became, largely shaping me. Many have said that, and I agree that seemed to be what Roddenberry was after. He didn't just want to show us men going boldly where no man had gone before. He wanted to take us there with them, in more ways than one.Your argument isn't, the overall picture here is, it wasn't a criticism, more an neutral observation.
My case is that the Federation has never been meant to be perfect, it's a backdrop for ethical dilemnas, which requires people to be trying to do the right thing but not always sure what that is. Those dilemnas are intended to make us think.
Clearly in your case it has worked, as you are looking very closely at the moral implications and drawing some well thought out conclusions. Where this becomes circular (perhaps wrong choice of words) is that the very fact of you posting this thread is indicative of the show having done it's job. You are stating the Federation is far from perfect, and I completely agree, but in doing so you are effectively standing as an example of exactly what the show is trying to achieve, intelligent people asking questions that reflect the world we live in without the emotional baggage of being directly about that world.
It's a shame these new reboot films don't have someone like Roddenberry behind them. They're not exactly very inspirational or educational.