He thanked her for caring so much about him. For Sasuke who lost his family at such a young age being loved by someone to such a degree probably meant a lot to him.
Love. He cared for her, I think he treats her the way he does. Out of love really, he knew to get a powerup he had to vanquish his love, maybe he ran away not only to seek Orochimaru, but to cut ties to Sakura.
It said somewhere that Sakura was one of the people that saved him from darkness and lonliness. Also that his work of thanks was not a lie. You know how much Naruto and Sakura annoyed and bothered him he really cared deep for them. But as someone else said, he had to break the bonds he had with Sakura (and naruto) to get stronger.