I'd make him pay it back with chores or through docking his allowance or whatever works in your home. I think it'd be a good lesson in responsibility, not just for sneaking around but also that when one runs up debt, it has to be paid.
That said, what's up with the school? How on Earth do they allow a debt like this to be run up? Do they not have some sort of system?
I'd suspect, having had 3 boys, that perhaps especially at this age, buying lunch is at least partially peer-driven. Maybe his friends get hot lunch. Maybe it gives him a feeling of independence, buying it instead of having what mommy packed. 11 is a funny age.
Along with paying it back, I'd sit him down and have a talk. Let him know that lying will not be tolerated and neither will surprise lunch debts. Oh, not to mention the food waste. I say put it on him. Show him how to make his lunch, he's 11, he can make a sandwich and toss an apple, some juice, and whatever in a bag (under supervision of course). My thinking is if he's responsible for having to make it, he'll be more likely to either eat it or let you know he'd prefer hot lunch. And set a weekly/monthly budget for hot lunch. Monitor the spend with him so you both can be on top of it and when it's gone, it's gone.