I agree with you in part. I never really read the grandparent's themes of "don't mess with nature, scientists full of hubris!" from Flowers. To me it was just a beautifully sad story of gaining something precious, and then losing it, while watching yourself lose it, piece by piece. The idea that it's not something external and tangible, but is a story of mental faculties, makes it all the more tragic.
And we can draw parallels to conditions like dementia. Charlie experienced a full life of learning and decline in a matter of a few months.
I do think of this as a science fiction story. Not "hard" sci-fi, but still sci-fi. To me it's the examination of what a scientific achievement could do, but for a fatal flaw. I think it is interesting and important to the story that Charlie's experience was caused deliberately, and not through an accident or other means.
His change could have easily been caused by something else besides science like a head injury that magically and temporarily reversed his handicap. And the story would have still been beautiful.
It’s more like a literary device; deus ex machina followed later by diabolus ex machina.