My older daughter has never liked tomatoes and says the smell of fresh tomatoes makes her sick. I've always encouraged her to respect/listen to her body's instincts -- I believe if her body is telling her to reject it, then she's better off not eating it. She DOES enjoy ketchup -- when she was about 2 or 3, there was a time when I said "only vegetable she eats is ketchup" but she's never wanted to eat tomato/pasta sauce. On the other hand, she eats pizza, but pizza sauce is usually made from tomato paste.
Maybe the thorough cooking process breaks down whatever bothers her about tomatoes.