You're right, I think, that the writers weren't always successful in avoiding the "I'm morally rightous, you're not, and so I shoot you" implications, but I was grateful they tried.
Hmm...sounds like TOS when Kirk comes down to a planet, basically says "You are wrong" and goes about completely changing their society.
Well, let's just say all the shows were on occasion unsuccessful at avoiding those implications.
Archer = "I'm morally rightous, you're not, and so I shoot you, or get my dog to pee on your trees"
Kirk= "I'm morally rightous, you're not, and so I rearrange your entire society on my whim"
Picard= "I'm morally rightous, you're not, and so I shame you with a long-winded speech that leaves you hanging your head at your failure to match my ideals"
Sisko = "I'm morally rightous, you're not....hang on...well, maybe we're both a little shady...shall we just shoot each other?"
Janeway= "I'm morally rightous, you're not, and so I am disappointed in you and may become a hardass or may just perse my lips and go away"