There is support to encrypt wallets in the test MultiBit code, which is available at:
https://multibit.org/releasesThe latest version is 0.5.7beta but there should be another version out (0.5.8beta) in the next day or so.
It is fairly mature code (I use it for real) but it needs some more review and merging into bitcoinj before it gets posted as the main MultiBit code.
As long as you keep backups of your wallets you should be ok using the encrypted wallet code. The best way to backup your wallets is to export the private keys using "Tools | Export Private Keys" into a password protected file.
If you did not want to use the test code then another way to keep your wallets encrypted is to have a trucrypt folder with your wallets in and only mount the trucrypt container when you want to use them. This is not as convenient though and has your private keys decrypted for longer.
