Weirdly, at first, I wasn't very comfortable with Michael coming close to outright calling the New Eden residents' beliefs irrational (maybe I was just afraid of how they'd react), but then I felt more perturbed that Pike was so determined to preserve their ignorance, even going so far as to basically gaslight poor Jacob. I did ultimately like the episode, though; the colony of transplants from Earth and Prime Directive quandary felt very "Star Treky"; I just came close to having a more negative opinion of the story until the scene were Pike let Jacob know that he wasn't crazy.
I think I pretty much agree with this. I think this episode might call for a rewatch on my part to be honest. There were definitely bits where I felt this uncomfortable kind of feeling that you describe where I was worried that it might turn 'preachy' one way or the other in a very unsubtle and unsatisfying way, but in the end I think they handled it pretty well. You can tell that both Burnham and Pike have valid arguments to present but you can also tell likewise that both arguments have flaws. Its a genuine moral dilemma in a very star trekky way but one that treats the audience intelligently and as capable of coming to their own conclusions about the merits of each position without forcing a moral down our throats in a way that a Berman era prime directive story would have (What's that Enterprise episode where Phlox basically condemns an entire species to die because of the absolute morality of the prime directive which doesn't even exist yet?). I much prefer the implication here that morality is actually a bit messy and there aren't always hard and fast rules and regulations that tell you what to do with absolute certainty; there's problems with Pike's faith in the prime directive as much as with Burnham's certainty that the colonist's beliefs are totally irrational.
The thematic stuff I think shows real potential; just as the Federation have almost god-like technology compared to the colonists, so the 'angels' have apparently god-like technology compared to the Federation; its just a matter of relative technological advancement. But it also doesn't necessarily reject religious belief as superstitious nonsense either, instead making it clear that both religion and science are both aspects of the human desire to explain the world in which we live, albeit both imperfectly. I had worried that this season might pit science and faith against one another in a heavy handed kind of way, but this gives me hope that it might be treated a bit more subtly as a 'both/and' rather than an 'either/or'. I really hope the handling of this faith/science theme continues with this kind of intelligence and nuance as the series progresses and doesn't go backwards from here.
Another interesting aspect of this episode was the interplay between the science/faith theme and the prime directive morality/non-interference stuff, with its overtones of scientific objectivism on the one hand and compassionate humanism on the other. I wonder if this will come to play an important part of the arc plot as the season progresses? Might the mycelial network be a kind of threshold for entry into the next level of cosmic citizenship just as warp is for the federation? Is the mysterious signal some kind of first contact test by the red angels? Do they have their own kind of general order one or non-interference directive? Obviously they have the ability to save species they believe to be in danger of extinction and don't mind a certain amount of exposure, arguably just as much as the discovery crew demonstrate themselves. The angels don't seem to stick around to be worshipped either, so presumably this isn't their motivation at the very least, unlike Apollo and some of the other godlike aliens from TOS.
I'm really digging the return to semi-episodic adventures, a very TOS flavoured transplanted human colony, more ensemble action from the cast, but with a modern sensibility and serialised characterisation and a slow burn arc that ties nicely into the story of the week. This season so far (and I know, its only two episodes but still) is reminding me of DS9 in a very good way, and it definitely feels more like star trek than last season but without retreating to late nineties nostalgia as a crutch. I'm becoming cautiously optimistic hahah! Mount is absolutely killing it as the wise but quippy Pike, I'm kinda hoping they keep him on next year to be honest, canon be damned

Some of the dialogue is still a bit cringe and info-dumpy, and Tilley's definitely
a lot in a way which... I can't really tell if I like or not? But I'm appreciating the increased number of little character moments between the tech-the-tech to plot-the-plot scenes.
I'm still not totally convinced by the spore drive, particularly given the 23rd century setting, just because it seems like such a god-mode technology, but maybe that's what they're going for and at least they're having Pike hang a lampshade on the ridiculous magical mushroom engine. I just can't help hearing the voice of Kathryn Janeway in the back of my head screaming at the f*ckers who classified the tech that could have got her ship home in about 20 seconds every time they fire the thing up.
This turned into a wall of text but
tl;dr: noice. much star trek.