That protects you if your computer is stolen. It does not protect you against wallet stealer trojans or viruses for the same reason that the wallet tools do work: the key is always stored in memory and Windows will decrypt it on the fly whenever any program wants to access it.
You should either decrypt your wallet when you want to use the tools, or store your wallet in an encrypted container (TrueCrypt, FreeOTFE, Bitlocker with a USB drive) that you only unlock when you use it.
Thanks, that makes sense. Sadly, I have not found a way to decrypt the wallet file after the Bitcoin software encrypts it. At most there is a temporary unlock function through bitcoind, but that still keeps the wallet in an encrypted format