I had what sounds to be this exact same thing. Only 2 differences is that mine is an MY03, making it older, and also my rust was right at the front where it meets the windscreen so the bodyshop thought that when the windscreen was changed the person was usiing a sharp tool that let water in although they saw no sign of a break in the paint (all rust was contained under the paint).
Cost me £250 to get it done at a local bodyshop that did a great job. Would recommend them to anyone in the souheast!