Yes, "The Magician" refers to the Dark Archer himself as played by John Barrowman! I have long known that he went by Merlyn "The Magnificent" so when that thought crossed my mind I googled "Merlyn The Magician" and What do you know, it turned out as one of Merlyn's several aliases. This was further listed in the "notable aliases" section of his DC Wiki and Wikipedia pages. Also, Marc Guggenheim himself updated his earlier post with this hint.
Full disclosure: "The Magician" does NOT refer to Zatanna. That'd be awesome, but refers to a different character. Hint: @Team_Barrowman
So in essence he pretty much gave us the answer.
So what do you think? And what does that spell for the milestone episode for Arrow? Sound Off Below!