This wasn't the first episode in TNG to center around the routinely-defied Prime Directive, but it was definitely the first one to actually be enjoyable. It was also arguably the best episode from the beginning of season 3 (though you could make a case for "The Survivors").
It's a testament to the improvement of the show that two ideas that had repeatedly tripped up the writers in earlier seasons - the moral dilemmas generated by the Prime Directive and the supposed moral superiority of 24th century humans - actually turn out to be strengths here.
While the anti-religious theme of this episode is somewhat strident, it actually makes the episode a lot more interesting because of the role into which Picard is thrust. The interactions between him and Nuria - particularly the scene in the observation lounge - is probably the highlight of the episode.
And it's nice to see how the Enterprise, confronted with a violation of the Directive, is forced to come up with ever more elaborate plans to correct that mistake - each of which fails and compounds the problem. Life doesn't always work out too neatly.
Two other observations - while Dr. Crusher's role in the episode is quite small, the tension between her Hippocratic Oath and Picard's obsession with playing the book sets up the rest of the episode nicely. And the actors who played the Mintakans - particularly Nuria - did a good job, certainly much better than the flunkies who appeared in "The Ensigns of Command".