There has been some discussion about the user's ability to read and understand contracts. This is already very apparent with a relatively simple financial instrument or DAO contracts and will become more apparent with advanced contracts and a wider community.
I have noticed playing with http://multisig.info:3000/
that comments are sort-of supported at this time. They are not mentioned on the CLL page of the wiki (https://github.com/ethereum/wiki/wiki/[English]-CLL)
or the whitepaper.
I would encourage both Python-style line comments and multiline comments. Clients could then automatically pull multiline comments at the top of a contract as documentation, or use conventions like using the line comment after a "stop" command as an error message.
The size of the comments shouldn't be a security concern if there is a hard size constraint on contract size. I can't think of too many additional downsides.
I can try to prepare a pull request for the CLL parser code, but wanted to solicit feedback first.