Exactly right! Well said.
I don't remember Darwin mentioning a gene splicing machine in his theory.
Y'all noticed this, but you, PH have got their number.
No. It's true that the genetic change itself did come from an intelligent source. But we know such a change could come about through random mutation, if we observed nature for long enough (we know random mutations happen, that much is really not up for debate). But the mutation itself is not what is really interesting.
The insects themselves have chosen not to breed with each other (for the most part, at least--the article said they "preferred" their own kind). Once the scientists set the mutation in motion, the flies themselves have separated themselves out. This sexual isolation between the two groups is not the result of scientists keeping half the flies in one cage and half in the other, but is the result of choices made by individual flies.
In other words, evolution does not require top-down management from scientists or a deity. The individual actors themselves will organize into species without top-down interference.
Of course, the actual speciation has not yet happened, and that will probably take a while (it will probably be more than just a few generations before they are physically incapable of mating). Still, this experiment is pretty big news.