Going back to the original topic ... from what I've seen and heard, you are expected to eat everything that you get with your kyuushoku - it's considered rude not to, and the students have to eat everything so you'd look bad leaving lots of food.
However, in many cases it is possible to bring your own lunch to school if you'd rather not eat the kyuushoku. I'm vegetarian and my base school is a senior high, so I don't have to worry about school lunches there - the students all bring their own food and eat in their homerooms, and the teachers bring their own food and eat at their desks. Everyone's happy. However, I also rotate between four elementaries and a junior high school, where the students and teachers are all served exactly the same lunch and eat together, either in a canteen or in their classrooms.
My base school must have notified all the other schools in advance that I'm vegetarian, it has never been a problem - from the start they knew that I wasn't going to eat the kyuushoku. I take my own lunch and usually heat it up in the microwave whilst the children are serving out the kyuushoku, and then I go join them - either in the canteen with all the other students, or in one of the homerooms. I did feel a little self-concious at first sitting there with my tupperware of Thai curry or whatever whilst they all tucked into their udon, but the children are often really interested in what I'm eating, and the teacher usually asks me what it is and announces it to the class. Once a teacher even helped himself to a mouthful of my lunch without asking me - was a bit of a surprise!
If the kyuushoku has things in it that I am able to eat (such as a salad, vegetable soup, fruit, some bread or a dessert), often I'll get a serving of this even though I've brought my own food, and I normally get given milk as well. It's a pretty good deal to be honest! I was a bit worried that I'd cause some problems, but no one seems bothered or angry or insulted that I am not eating the same lunch as everyone else. And I definitely don't have to hide myself away from the children so that they don't get jealous - I eat with them.
I think if you really don't want to eat the kyuushoku, you should make it clear from the start that you'll be taking your own lunches to school everyday - you can't just change your mind if you see a lunch you happen to like the look of! If you do opt for the lunches, though, be expected to eat everything they give you (unless you're able to sneak it to someone else!).
