For what it’s worth, I share a lot of your concerns. I always say my faith hangs by a steel thread - it’s the most accurate way to put it.
However, I read over the article you linked - and honestly, I didn’t find anything in it that truly shook me. Your problems seem to center around assertions by the Church that only humans have an immortal soul, and the reasons why they came to such a conclusion. First, I’d love to see where the Church speaks about animals in regards to things like that - from my understanding, the point that is mostly made clear is that humanity is entirely distinct in terms of capability and mental/spiritual endowment, and has a purpose beyond what animals have. Other than that, it’s speculation and nothing more; an area of debate, such as limbo. (Though there’s an entry on
newadvent.org regarding cruetly to animals - animals are not ‘things’ by even loose Catholic belief.)
I don’t think recent scientific development is the first time it’s been pointed out that other animals have some capacity for rudimentary tool use, communication, etc. And I don’t think said development has shortened the gap between a humans and the next ‘closest’ animal by any real degree - humanity isn’t what it is purely because of a capacity for language, or a communal spirit. We are capable of conceiving things that no other animal could ever hope to, desiring things that they could barely understand. Most importantly, we can understand concepts of good and evil, right and wrong, and not just ‘pain and pleasure’.
That millions of years ago the human species (or what it used to be by way of ancestry) may have been at a different stage doesn’t upset me. We can only be vaguely certain of what capacities ‘our ancestors’ had, what their limitations were compared to where we are now. Certainly, something major and considerable happened at one point in our development, and fairly recently by any standard. What the change was, when it happened, and how it happened… that’s perplexing. Even in that article there was a lot of interior debate, on everything from cross-breeding with chimpanzees millions of years ago, to what was the reason our brains have become what they are.
The Church’s position on the origin of man, as near as I can tell, is that at one point mankind as we know it came on the scene, and the ultimate result was a fallen state. It could have been a ‘big bang of human consciousness’ - the point where we crossed the divide from merely experiencing ourselves and our environment, and suddenly began to realize that certain things are good, and certain things are evil, and that we can in fact choose evil if we like. Whatever that point was, it effectively marked the end for traditional evolution for humanity. We continue to evolve, but in dimensions that simply are not covered in the animal world.
That, to me, is one of the strongest arguments for the Church’s view on things. It has always viewed humanity as an oddity among the rest of creation - a kind of creature apart from all the others. Science continues to illustrate this.