Answer:
Yes, he did. It is shown in the game that he loved her deeply; it was his horrible memories of his past and his own self-loathing that kept him from getting too close to her. At the end of the game, he forgives her for everything she did and they try to start a new life together.
Their relationship is expanded in MGS4, where it is shown that they continue to love each other despite everything that happened between them. They reunite in the end with their son and start over as a family.