I'd love a Togepi CD, but given how it's shiny has already been released, it does seem pretty unlikely. But Niantic does what Niantic wants, so who knows.
I think the most likely path for Togekiss to get Fairy Wind, is to put it in a raid day like Gengar. A 3 hour raid day for Togekiss with Fairy Wind sounds pretty good! I'm personally just hoping they update the GameMaster and just allow us to TM it to Fairy Wind but we'll see. I do think, it will be in the game soon though.