It is stated specifically that Flynn's exit was placed far away from the population to avoid stray programs from
wandering in. This implies that any program could have exited if they had access to Flynn's disc.
It is also stated the CLU has found a way to not only bring himself, but all of his minions into the real world. He places Flynn's disc in a holder high in his ship, presumably so the exit effect would take everyone on the ship with him.
If there was no danger of letting programs (or ISOs) rematerialize into the real world, Flynn wouldn't have had to make the necessary precautions of placing the exit far away, and requiring his data disc.
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.