Conflicts in Utopia?

I think you don't have to take sides when discussing if Deep Space Nine's more conflict-laden relationships went against Roddenberry's dream of a utopian future or if it highlighted the complxities of cross-cultural communication, social and business interaction. 

Roddenberry's utopian vision was basically about the future of mankind, and all crews encountered civilisations that have not or probably will not change and become the communism-like civilisation humans live in in the Star Trek universe. Some other civilisations have lived in long-standing conflicts or have been at war with each other. In the case of Deep Space Nine, Captain Cisco has to learn, sometimes the hard way, how to deal with conflict that doesn't exist in the human utopia anymore. In the Next Generation, Captain Picard may be the ultimate diplomat, but even he encounters huge tension or major conflict that cannot be solved easily.

I think the presence of conflict is a good reminder also for people trying to support inclusion in our present human world, too. We need to have tools and also develop some kind of reaction to groups that live for conflict, that want to exclude others or themselves. For an open person, it is shocking to encounter this, and tackling these topics in a fictional world helps us think and also probably develop strategies. It is easier as it is, again, done by defamilarisation, and it is much easier to be realistic and objective if you are not personally involved or emotionally invested.