I truly believe he meant that "Thank you". He was grateful to all she did for him(cried for him, comforted him etc), but wanted to end it there and then. Which worked, because 2 years later he is completely indifferent to her.
Actually , this was a real moment between them , even though her confession was genuine and all heart it was so selfish can measure it up to anything . He denied her feelings though before she even said '' i love you with all my heart'' but she did it anyways, so yes he thanked her for crying ,caring , but that's it , nothing more. He cared for her as family something like a mom (sis) not being biased here but that's what he thought in his flashback when he was confessing , he thought of both of NAruto and Sakura not a moment they've both shared ..
Even in during the Gaara fight he told Naruto that he must protect her , because he cant afford to lose the people aka his family who he cares for .
Edited by Psychox, 16 August 2013 - 07:53 PM.