I doubt you're gunna see anything good come out of this. Mostly because, it just "feels" like there is, or possibly, a good logical explanation involved.
A lot of things in life that seem stupid, are there for a good reason. And to win your case, you best not go ranting and crying, otherwise you sound like a baby. Which, if that happens, all hope of future success on this case would be lost.
The only true way to combat this is to ask questions. "Why has this issue come before the board?" "Is there sufficiant back up data that helps enforce the oppositions sudden action?" "How does this affect all other personal items brought to the school... i.e. Wallets, personal books, their own CAR, etc."
I think that if you look at the situation with an open mind, and create on honest objective opinion based on all the facts, then you just may be able to come up with a better solution. So not only do you get to keep your guitar.... but also look real good in the eyes of the school council..... which just may help you in the future (believe it or not, this stuff really does come back to you when you least expect it)
Whatever you do... don't lose your temper. That should be the last resort.
Good luck!