I agree with you up until you get to acknowledging reincarnation as an acceptable ending in any regard even in the slightest.
As I said in a post I just made. If the idea Nishigori was working with is "love transcends" then he showed that with the Mitsuru and Kokoro mindwipe. Though I think that was poorly done because it was clear that they would get back together and literally nothing about their relationship ended up changing. But if that's what he really wanted to do, then great, point made: LOVE TRANCENDS. Now we could talk about how characters overcoming a mind wipe is completely unoriginal and has been colored ad nausium and how two characters dealing with pregnancy and upcoming parenthood who were raised in the manner that the parasites were would have made for a much more compelling arc for the two of them, but we probably don't need to.
Again the point has been made that LOVE TRANCENDS. Now we have Hiro and 02. Their love has conquered and they are out pushing back the not anti-spirals. As you said, they are the main duo, the reason most people are still watching the show is to see their love prevail. What Nishigori could have done is have them beat the not anti-spirals and make their way back to earth to live out a peaceful life back on earth with their friends. Everything would have loved it, it would have felt cathartic to see them back on earth after their friends were building society back up and the message would have still been present in that LOVE TRANCENDS all odds and they can finally be free to love eachother.
But what does Nishigori do? LOL THEY DIED. YOU SO SAD NOW, I AM GOOD DIRECTOR. And after a full episode of epilogue material about the side characters we get LOL JK THEY REINCARNATED after you're already mad that he killed them for no reason because had they made it back to earth it would have been the same message that wouldn't have pissed 90% of the audience off.