Thanks. I am in the process of moving my P2Pool so I can use pywallet and leave my bitcoin-qt shutdown for a week or so, hopefully the it will be removed from the blockchain then so I can resend it with the correct amount, then move my P2Pool back.
Yes it will eventually time out and you will get your coins back, unless it happens to get mined by someone who doesn't care about the fee.
Minor correction to your terminology though. It isn't in the "blockchain" just the memory pool (collection of unmined transactions that have been sent).
EDIT: You still need to remove the transaction from your wallet so you can resend, which seems most easily done by (temporarily) creating a new wallet and importing the private keys for all the inputs on the transaction. That sounds like a pain, but it is what it is.