I made several backups, I'm going to try and delete the transactions using pywallet and rescan. Is this an appropriate course of action? I don't think the wallet is damaged.
Yes, it is. Although sometimes the balance shown by QT client does not adjust well, even after a rescan. Happened to me, I had to import the private key to another wallet and send the coins back to another address of the first wallet for it to show the right balance.
G'luck.