Crucia gains a human form to enter the Shaper Citadel, or whatever it was called, in Morban and take something from Kain and the Shapers that she needed for the Infinity Gate. She could only enter the place with the human form. You'll see at the end of the Morban storyline. So yes, the half-naked queen you see in loading screens is Crucia.
I don't think the game explains at all how she did it and why her form looks like the queen. Unless it's something that happens in the raid.