Flynn spoke about Quorra as a solution to all of the real world's problems.
Kevin Flynn: Yeah. The last ISO.
Sam Flynn: All this time, you were just protecting her.
Kevin Flynn: She's the miracle, man. Everything I ever worked for. "A digital frontier to reshape the human condition."
Sam Flynn: I always thought that was a plug line.
Kevin Flynn: In our world, she can change everything.
This leads me to the conclusion that she didn't rematerialize as a human. Or maybe she is the perfect human, with no flaws (ie such as maybe no genetic flaws, or perfect disease immunity or something). I don't think she is an android, if a program came through it would just try to complete its programming. Perhaps she is a new lifeform that takes on the shape of a human.
This is the same answer I gave to a similar question on Movies.SE.