Hi Rory - I agree with your point about the Fall — the fact that dinosaurs preceded humans makes it difficult to argue that they experienced pain because the first humans got something wrong.
The progress scientists have made, using logic to understand the universe, is grounds for thinking that its Creator (if it has one) is either constrained by logic, or else chooses to do things in a logical way. Even if doing things in a logical way means hurting someone.
Olaf Stapledon's vision or dream of the Star Maker is in some ways quite different from the way Christians normally think of God — so much so that C.S.Lewis characterised Stapledon's vision as "sheer devil worship".
One important similarity between Stapledon's Star Maker and the Christian God is the idea that pain is experienced not only by created beings, but also by the Creator himself. That is, Star Maker doesn't just sympathise with suffering beings, he actually shares their hurt.
I've used the pronoun "he" because Stapledon uses this. Yet it seems to me that Star Maker has distinct similarities with the Hindu vision of Kali, who is a "she".