Harmonia is a story in a post-apocalyptic setting where robots who are capable of emotion turn out to be more "human" than actual humans. It's not the first of its kind and certainly not the last. As it should be. After all, us humans really need to be constantly reminded of what it is that makes us human, since we tend to forget it quite easily. You could even say that the ability to have feelings is where human greatness comes from. The other humans in Harmonia did little more than kill, steal and destroy, while Rei, being a person with fully developed emotions, managed to help others, to bring them happiness, and even to literally rebuild and restore their world. Forgetting all emotions (Harmonia) or concentrating on the negative ones (Planetarian) is a surefire way for us to go extinct.
While Planetarian is more about rediscovering and nurturing what little warmth is left in a world that has ended, Harmonia, goes beyond that and concludes the story on a more hopeful note, where said warmth becomes a means of reaching a future of harmony happiness.
I really enjoyed Harmonia and the beautiful visuals exceeded all of my expectations. It was not exactly a mind-blowing or heart-rending experience, but definitely a time well spent. I was skeptical about the unusual text placing, but it turned out to work perfectly.
What I liked the most was the gradual "revelation" of Shiona's "dark side". Despite several hints being dropped here and there, her behavior in chapters 4 and 5 came as a huge surprise in terms of how far she has gone with her personal agenda. Good thing I'm familiar with these kinds of situations in Key works, or I might have ended up hating Shiona.
But really, thinking about how Tipi was all alone in the library, crying, while Rei and Shiona were being lovey-dovey left a bad aftertaste.
Expecting a real-world religion to play any kind of role in a story in the anime culture is weird. It's a rare occurence. Normally, the author just borrows a few characteristics, concepts or legends to build his story and/or characters around. So a motif is usually all it is. A nun is a woman that wears a certain uniform, does certain things in certain places and is associated with certain personality traits, just like a nurse, a stewardess, etc. For all we know, Hinoue probably just wanted to draw a certain outfit and that's how Shiona's character design came to be.
The bookclub did discover a lot of christian themes and imagery in Planetarian, but that's one of those rare cases.
So I don't see anything to be disappointed about.
I believe it was necessary given the story's length and also in order to drive the point home that we can become dependent on a single feeling to the point where we would break if we were to lose it.
I did get LB vibes, but not the ones you did.(Little Busters spoilers) You see, what Kyousuke did to Rin was dragging her out of her comfort zone in order to make her stronger. Shiona, however, acted purely in order to preserve Tipi's current fragile state. That's almost the opposite of your example. I think the same as @cjlim2007 onthis one: What Shiona did to Tipi was the same as (Little Busters spoilers) how Kanata acted in front of Haruka. She fuelled Haruka's negative emotions, which were one of her few pillars of support, while taking away her new-found hope, which Kanata believed would destroy her sister in the end. All the while, Shiona/Kanata acted as the bad guy.
And it's precisely because I remembered this that I decided not to be hasty and make the same mistake as I did back when I was reading that particular LB route: Hating the "evil" character before knowing their true motive.