No, it isn't evidence of that. Drosophila and Caenorhabditis are not our ancestors, and they're not intermediate species, they're way off on other branches of our family tree, branches that are likely at least 600 my long.
The common ancestor of corals and humans had the gene. That creature would also have been an ancestor of nematodes and arthropods. The gene was lost early in the lineage of nematodes and of arthropods, but retained in the primitive chordates. It's not the first example of this.
Oh. I was worried for a minute there that I might not be related to pond scum. It's comforting to know that my pedigree is intact.