Wow! There's so much here I want to comment on, so please bear with me....
If memory serves, the Mintakans reverting to their old ways in Who Watches the Watchers entailed sacrificing people, among other things.
I've just re-watched
Who Watches the Watchers. That pained me, since it's one of my least favorite episodes of the entire franchise. The Mintakans don't revert to sacrificing people. It is suggested by certain Mintakans, but ultimately rejected by the rest.
As far as Trek in general, I've always thought that humans have grown up to a point where people can believe what they believe without a need to shove it down everyone else's throat, like quite a few people today. I mean, without people to be attention whores or running around calling other people bad for not believing what they believe, it wouldn't get much exposure since any religion is a pretty personal experience for the one concerned.
That doesn't seem to be the prevailing attitude on DS9, at least for some. The episode
The Reckoning shows how some 24th century people still try to shove their beliefs down people's throats. Sisko, by this point, is a firm believer in the Prophets and is willing to do what he does in the episode based on his faith. At several points, Dax flat out ridicules him about his faith and for not believing there is a scientific answer to what's going on. At another point, Bashir laughs about how the prophecy could even be considered to be anything more than a fairy tale.
Had Picard kept his argument SPECIFICALLY to the Mintakan people, and the fact that they made a choice and the cultural contamination overrode the choice they made of their own free will, I would've agreed. Belief must be by choice, not by coercion. The trouble was when he made the sweeping comment about humanity and all other races, that religion is something all races must evolve past. That was quite bigoted, not to mention hypocritical out of the mouth of Mr. Tolerance and Relativism.
As I recall, he said nothing of the sort. He said he would not send them back to a primitive age of fear and was very emphatic about it.
What he said, exactly was....
"Millennia ago they abandoned their belief in the supernatural. Now you are asking me to sabotage that achievement?! To send them back into the Dark Ages of superstition and ignornace and fear?! NO!"
Sounds like a sweeping generalization to me. Sounds pretty bigoted as well.
They did mention Chistianity as still going on in "Cold Front"
Which is the it should be, IMO. Phlox states that he attended a mass at St. Peter's in Rome in order to familiarize himself with Earth's various religions. It's there, it's stated that religion still exists, but it isn't dwelt upon, pro or con.
So maybe if Darwin was a priest or soemthing as well, religious people might give him more credit, I guess.
I'm a fairly religious person, and I give Darwin credit. Evolution, and science in general, is not incompatible with religion.
It all comes back to the same old fallacy, that the person is just as or even more important than the words they say. I don't care who said the quote in my signature so much as the truth of the quote itself. It doesn't matter that either Plato or Socrates might be a fictional creation of the other, the words still hold true. Jesus, however is different. Who he claims to be is not separable form his words.
So, are you saying you can't believe in words like "Love your enemy," "Turn the other cheek," "Do unto others as you would have done onto you," ""He that is without sin among you, let him first cast a stone," or "Blessed are the peacemakers" because you don't believe in the divinity of Jesus?
But those atheists (because they have no dogma) are not doing it for the cause of atheism. The same cannot be said for those that perform crimes on behalf of religion.
Ummm.... yes they were. They forced people to be atheists because it's what they, the powers that be, wanted them, the people, to be. It's the exact same thing as a religious dictator forcing all the citizens of a certain country to be Chrisitians, or Muslims, or Hindus, or whatever.
Atheism in and of itself has no dogma. Sure those people and those systems were wrong. But it still doens't change the fact that atheism itself has no dogma and that none of those acts were committed for the cause of atheism (they might have been committed by people who thought they were acting for the cause of atheism. But in that case, only the people committing them could be blamed, not atheism itself.)
Then why should religion, in general, be blamed when someone distorts it to serve their own goals?
I'll end with a favorite quotation of mine....
"Science without religion is lame, religion without science is blind." - Albert Einstein