It sounds like a good approach.
I quite agree that she shouldn't be made to say prayers before lunch, unless the prayers are in a form that you feel is suitable - a lot depends on how it's worded, I see no problem myself with a simple acknowledgment of gratitude for what is in front of us, maybe you'll find that the form they use is acceptable to you or to your daughter. But if your daughter doesn't feel comfortable with their prayer (yes, she's young, but she may still have feelings about it) they should at least let her miss out the reponses if she doesn't want to join in, and they should make sure that she doesn't get picked on about this.
But I do know several pagan mothers who've managed to reach a good accomodation with religious schools about this; to some extent, it's been as though they were happy to have another parent who had (what they see as) some form of faith, rather than none.
By the way, in case this interests you: I don't have chapter and verse on this, but I was told by Steve Wilson of PEBBLE that schools are supposed to include the faith of every child in the school in their RE syllabus. So if they have a Hindu child, they must teach at least something about Hinduism; and if they have a pagan child, they must teach something about paganism. As I said, I don't know the details on this. It might be easier to offer it to them initially rather than demand it - maybe you might get to be the one who did the assembly! In the end, though, they have an obligation to include every child in their school, and that means (among many other things) sympathetic treatment of the faith their parents practise.