If you are using OS X there is now an option to store your Beanstalk password in your keychain. Follow the steps below to create the keychain item. The script will then access this keychain item rather than the password in the config file.
Open Keychain Access (located in Applications > Utilities).
Select File > New Password Item...
In the Keychain Item Name field, enter beanstalkcli
In the Account Name, enter beanstalkcli (this needs to be exactly beanstalkcli)
Enter your password in the Password field
Now you can configure the script. Fire up Terminal and type
beanstalk -m account:config
You'll be prompted for your beanstalk username and account name. You'll also be prompted for access to your Keychain. Click Always Allow to continue.
That's it, your password is now stored within Keychain, rather than in a plain text config file