When Namine placed the memories in Sora, it pretty much made him see her as more then just a friend, Then when she told him the truth he seemed to like and care for her more.
Because he appreciated her honesty.
Do you think he cared for her more because he figured about how lonely and painful it might of been, and he saw the memories as being something she really wished she could of had?
It was a mixture. He saw someone he came to care for dearly, saw that despite it all, this person was the same person as the one he 'remembered' and therefore still deserved his feelings, and she was someone who needed him.
Also do you think Namine just because she was lonely and wanted a friend, or did she actually start to develop feelings for him yet was horribly turned down by Sora when he wanted his old memories back?
Namine's the kind to put Sora before herself. Otherwise why help him? And why go to all this length to stay out of his life, knowing the risk her very existence was putting him in? Was she saddened when he chose the real Memories? Obviously. But like she told Riku when he refused to simply lock the Darkness up - she "hoped" he'd say that - I doubt she'd have been really happy had Sora chose to give up his real Memories for her. That's not 'her' Sora.
And now for some rant~
Canon fact #1
Sora's Memories of Namine couldn't have been originally of Kairi's as
1) Namine and Kairi act differently, confirmed by Nomura. It wouldn't have worked out.
2) The Promise Memory. Kairi only arrived on the Islands on the night of the meteor shower, yet for Sora and Namine (And Repliku and Namine, lol) that was the strongest, most meaningful Memory.
Canon fact #2
Whatever Sora felt for Kairi before CoM, whatever he felt for Namine was stronger as confirmed by Namine herself. Therefore, Kairi was always described by Sora himself to be a friend, but Namine to him, in his made up Memories, was
more than a friend.
Canon fact #3
Despite Sora reaching out for Namine and holding on when he "found" her, and making the promise to her with a pinky swear, he kept his distance away from Kairi in KH2, and then broke the contact with her - as opposed to Namine being the one that pulled away in Re:CoM.
Canon fact #4
Right before the Xemnas-armor fight, after their ride back was already destroyed and they were about to fight Xemnas because they had no other choice - sink or swim - it's hardly Kairi Sora thought about in what could've been his final moments - it was how he didn't get to thank Namine.
Conclusion: SoNami >>>>>>>>>>> SoKai.