I also voted "wrong girl, wrong place," but for a different reason:
Everyone in the Trilogy had freedom of choice, and made free choices. Kay chose to marry Michael, but I don't believe she actively tried to change him. Instead, she chose to believe him when he said that he would change, or that the circumstances of his life were changing around him.
The key scene, IMO, is when Michael went to New Hampshire to court Kay after returning from Sicily. She asks what happened to his vow not to be in the family business, and he replies that his father is "no different than any other powerful man with responsibilities toward others." Kay replies that Senators and Governors don't have people killed. Michael replies, "Now who's being naive?" He adds, "My father's way of doing business is finished. In five years, the Corleone Family will be completely legitimate." Kay buys it.
This scene tells me that Michael really wanted to be legit--but he alone would define "legitimate." Sure, Senators and Governors lie, cheat, take bribes and cause deaths (presumably by voting to send troops to war, or by cutting healthcare or welfare programs). Therefore, he's no different. If they can be considered "legitimate" while doing bad or illegal things, then he can be "legitimate" for his own malfeasances. I don't think Kay caught that subtlety.
Michael needed Kay, the ultra-WASP from a "respectable" family, as part of his quest for legitimacy. I think she saw that. She probably liked to think of herself as an "uplifting," or "reforming" force in Michael's life--a lot of women of her generation who married "beneath" them did. But their expectations clashed completely. That's why I count Kay as "wrong girl, wrong place." Apollonia would have caught on right away, and accepted Michael--and his life--at face value.
Kay eventually gets it. In the novel, Kay chooses to raise their kids in the Catholic Church. Michael is "disappointed" because he wanted his kids to be more "American" (i.e., Protestant). But in the last scene in the novel, Kay goes to Mass every morning with Mama, both of them praying for the souls of their murdering husbands. It's ironic: Kay adopts Michael's born religion because that's her way of dealing with his born nature. It's as if she finally accepts that he's a killer, and now believes that she can help redeem him from his sins.
GFIII has an even better denouement for Michael's fantasies of "legitimacy," and Kay's role: In his study during the party, he gives out another rationalization for his life of crime: "I spent my life protecting my family from the horrors of this world," he shouts. "But you became my horror," she replies, firmly. Right, Kay!