Is there an open source tool to publicly destroy bitcoins?
The most secure way to destroy bitcoins is to send them to a script that can never return true, and which includes the reference code that confirms the goal of destroying these coins. I don't know of readily available software tools that can do that, and I'm not sure the network will accept these transactions.

Here's a simple method everyone can try at home: Take the reference code, apply RIPEMD-160 and encode it as an address. Do a transaction which sends a satoshi to this address, and the the coins-to-destroy to 1BitcoinEaterAddressDontSendf59kuE.

To demonstrate my point, here is me destroying 1 mBTC - http://blockchain.info/tx/f374fb91ea29b02d295d535da537c7770caa71c4937095c51467b4d8b1b60c1b. Address is hash of https://bitcoin.stackexchange.com/a/7443/575.

Signing a message with the address used to send can also be employed as extra verification.