I suspect that she was so submissive and adoring of Khan that made her "special." Not only was her adoration of him a nice stroke to his ego but her being so submissive also satisfied his domineering personality.
Speaking from the BDSM perspective, not only is McGivers the perfect bottom, she also has the art of "topping from the bottom" down pat. By the end of the episode, she has wrapped Khan completely around her finger. Hers is the ultimate have-the-cake-and-eat-it-too award: she betrays Khan at his moment of triumph, turning it into utter defeat, and actually earns Khan's undying admiration for the act!
Khan may be egoistic, inexperienced and ignorant, but he isn't blind or stupid. If he's any good at his mind-fucking games, he will recognize he has been bested here. What better mother for his untold numbers of superior children (many of whom we probably see in ST2) than a woman who is his match in both soul and skill?
Timo Saloniemi