Nicholas Meyer says: "So VI is a film in which the crew of the Enterprise has all kinds of prejudice, racial prejudice, vis-a-vis the Klingons. And some of their remarks, including how they all look alike and what they smell like, and all the xenophobic things which we grappled with - that was all deeply offensive to him because he thought there isn't going to be that."
Frankly, I think this is misleading. I don't know if Roddenberry truly believed that within a span of a few hundred years humanity would have gotten beyond prejudice, and there's a hell of a lot more going on here with the Klingons and a potential treaty than simple prejudice - decades of war, destruction, deaths, etc. But I believe that Roddenberry believed that the crew of the Enterprise would have been, at the very least, a lot more professional then to express such feelings, and more likely to be enlightened enough to get past physical prejudices and deal with their feelings about the Klingons directly. Hell, the ability to do just that would be a basic survival trait for a Starfleet officer in the Federation - you're dealing with so many different alien species during often-crucial missions, that if you showed prejudice or distaste at every physical characteristic, let alone social characteristic that you didn't like, your career wouldn't go anywhere. I don't doubt that there are xenophobic folks in the Trek universe, I just don't think there are many, if any, in Starfleet, and I think there're a lot fewer of them in general.
I found the sentiments Kirk expressed at the briefing where Spock volunteered the Enterprise for the treaty negotiations really hard to swallow, given all that he's done in his career. I believe he was shocked, by the destruction of the moon, the Klingon's plight, and the possibility of a treaty, and I think he was furious that Spock volunteered him without consulting him first - both at the act and the lack of trust it implied. But I had a really hard time with the idea of Kirk being disgusted enough with the Klingons to want to just "let them die."
Roddenberry's belief in the perfectibility of humanity is one of the things that draws me to the show. None of his characters actually get there, but they all try hard, and I think that's really important. Even if perfect is not possible (and depending on the timescale we're talking, that might be debatable), trying is what makes us better both as individuals and societies. If we don't try to be better, we inevitably end up in pretty poor shape. And we can definitely achieve "better," if not perfect. Isn't that worth striving for?
As for the no conflict, that's just wrong. Roddenberry set out to write SF drama, and you can't have drama without conflict. He knew that. What he didn't want was to take the easy route, a shoot-'em-up, violence-is-our-first-resort universe. There's all kinds of conflict in those first 2 seasons when Roddenberry had pretty direct control of the show. "The Naked Time" - fighting a disease and ourselves when infected with the disease (or generally when we're uninhibited). "The Enemy Within" - coming to terms with our own darker selves. "Dagger of the Mind" - conflict with others but by outsmarting them, not outshooting them. "The Menagerie" - conflict with our physical shells and fighting what we see as our ultimate destiny. The list goes on and on.
I'm not really impressed with the lack of understanding Meyers is showing here of Roddenberry's vision for Star Trek. It's not an accident that my favorite Trek is still the Original Series.