If you are using the version 0.4.21 then the compressed and uncompressed private keys are interchangeable. Earlier versions did not understand the compressed keys and could not import them properly. I'll update the file contents to make it clearer.
You can see which version you are on in 'About MultiBit'.
The encryption format for the private keys is OpenSSL compatible - you can use openssl on the command line to encrypt/decrypt. See the bottom of:
https://github.com/jim618/multibit/wiki/Export%20and%20limited%20import%20of%20private%20keys
It uses the OpenSSL key derivation function and 256 bit AES.
Ah, github, didn't think of that Thanks!