My (very) speculative answer is that Quorra is indeed a flesh and blood human. The laser in the original Tron was capable of "digitizing" matter into information stored in memory while suspending atoms or molecules in the laser, and then reconstituting the object at a later time (see here for a brief description).
Since Flynn and Sam were both successfully digitized and reconstituted using this technology, it stands to reason that Flynn could "build" a human being from scratch given proper ingredients (e.g., ~ 140 lbs of atoms of the right type and proportions: C, H, O, N, etc.) + assembly instructions. The assembly part would be difficult to code to say the least, but perhaps Flynn could use a shortcut by borrowing assembly code from other humans that had been scanned in.