^^ I agree with everything you say and you're right. It looked like she gave up on them and that really pissed me. Like I said before, Haley pissed me in S2 with everything she did and said... But:
I know Nathan was always supportive of her music and he didn't want her to give up her dreams for him. I know that. (God, I'm so bad at expressing myself that it hurts! lol) What I was trying to say is that when Haley told him she was invited to go on tour, you can't really detache Chris from the tour/Haley's dream from Chris. And Nathan knew that, either she went on tour with Chris or she didn't go at all (since Chris was one of the guests or whatever). So, by giving her the ultimatum, Nathan direct or indirectly, was making her choose between him and music, her dream. And it's there that I think he thought: "If I gave up HF for her, she must give up music for me, too."
Plus, I always saw that the only two feelings Haley had for Chris were envy (of what he had) and gratefulness (for improving her music). I never believed she had romantic feelings for him, like she stated so many times. But then again, I totally understand Nathan: he had just found out his wife kissed the creep and she just said in the following second she was going on tour with him. I understand him, but he was still wrong. Like Haley was the entire season.