We get the impression that Emma Watson almost never does anything that she doesn't want to do, so we're surprised that she decided to go ahead with kissing Rupert Grint. We suppose she couldn't really refuse to do so - everyone knew that their 'Harry Potter' characters eventually kissed in the books, and so it would have been impossible to avoid it on screen. Watson didn't' have so much as an issue with the scene as an issue with kissing Grint. She loved him very much - just not in a romantic way.
What's easy to forget about the 'Harry Potter' cast is that they grew up together in the world's glare, and the only people in the world who understood what it felt like that they could speak to were each other. Watson and Grint had a relationship like a brother and sister, and so kissing each other felt excruciatingly awkward for both of them.