Those are just basic principles of moral philosophy, not specifically religious, much less Judeo-Christian.
This, I agree with. But that's just an artifact of the Federation being a free society, like the United States, that sees value in letting people believe what they wish without interference. That doesn't mean any of those beliefs are necessarily of value on their merits, much less that their truth claims are valid.
Aack.

The most wince-inducing line from an already terrible episode!...
To be honest, I found all of the "Bajoran religion" aspects of DS9 deadly dull (and ideologically incoherent), and thought those story elements significantly undermined both Kira and Sisko as characters. But YMMV.
But even outside of Trek, the character trope of a protagonist who was orphaned and raised by surrogate parents is literally as old as fiction. Indeed, I'd venture that it's far more commonplace in fiction than IRL. It's been milked dry. What new insights does it have to offer? (I'm sure some real people can in fact relate to the circumstance, of course. But they're a vanishingly small percentage of the overall audience.)