You can use NTFS ACLs to protect the files from users who are not authorized to execute them. Users who are authorized to execute them, by definition, can read the passwords (in the obfuscated form, if you choose to obfuscate them). Access to execute implies access to read. If the script can de-obfuscate the password so can the user.
Assuming you're trying to protect the passwords from the users who are allowed to execute the scripts, what you're saying isn't possible. You're really saying:
We have passwords that we need to give
to users so they can use some software, but we don't want the user to
know what the passwords are.
By definition the user's has to be able to recover the passwords in order to use them. Any obfuscation or encoding of the passwords that you perform is just a "speed bump" for a determined user to find out what the passwords are.
So long as the execution context of this script is the user you have to give them the passwords. Whether you attempt to obfuscate the passwords or not is your business, but you're still giving them the passwords.