I agree that it's very respectable that you decided to boldly go with what you felt was the right choice even when it was a moment late and you had to stop, turn around, take a step back, and apologize before going on with it. Doing that takes courage, and most people would fake it or just feel committed and go with what they had already started doing.
That said, this is an alternate universe-centric story in a series with a comic that constantly presented us with "alternate universe" extras. I know you already said you're going to include the unfinished oops-ending, but I just wanted to agree that I appreciate that, and depending on how you want to look at it and what you want to call it, it seems like an "alternate universe" extra. I hope you include an explanation for anything the pictures don't tell us, though!
I must admit that, if I'm seeing what the split you're undoing is correctly- though it is just a guess-, I see benefit to both sides of the tale.
The more smooth, expected path, that Pho really is as earnest- if troubled and wracked with guilt at his past- as we thought him, has integrity and is easier to swallow. It still shows us that everyone made their mistakes and can commit atrocities for the most innocent of reasons, and it could be said that Pho and Kaye's seperate issues with the past mirror each other and reflect upon something.
The complex twist path, with an intriguing, viable if missable thread of little clues running back through the story, takes us to even more unexpected realms, though it may feel like a ret-con or potentially betray our hero of being any kind of hero (maybe). Then again, that direction sounds pretty noir...?
Of course, I may be totally and utterly wrong about what either path is, as remains to be seen- and I look forward to whatever we do see! I also trust in your vision and feelings in deciding that this way will be the better ending. It will be fun to ponder both, though, I think- infinite splays, infinite possibilities.
That said, I am still wondering if we find out what happens to Vola (the non-wobbly one)! Not that her fate wasn't a sight better than poor Virtue and Wailan (unless, of course, Heliotrope and Fuschia were heroic enough to stick to their word by overseeing eons of work, which I like to hope they would get around to at some point betwixt the thoughtform cakery and other adventures), but it begs so many more questions!