I'd like to see the core config command handle updates as well. For example, for updating WP_DEBUG, I'd run something like this:

wp core config WP_DEBUG true

(similarly to git config user.name Name).

A couple of quick notes:

• I understand that wp-config.php can contain arbitrary PHP and implementing the proposed functionality can be a bit tricky. My approach would be to strictly specify how the core config command works, for example, only supporting simple constants and putting them right before require_once(ABSPATH . 'wp-settings.php'); or something like that. If the file structure doesn't conform to what core config expects, it would do nothing and only print an error message.
• Was thinking whether there should be a separate (sub)command for this but I think that the core config could be used for this seamlessly.
• Data types would need some attention. For example, the example given above (updating WP_DEBUG) would need to correctly put a boolean into wp-config.php while in other cases, strings or numbers could be required. I think that most cases could be handled automatically but there could also be switches like --bool or --int, similarly to what git config supports.

What do you think? I'd be willing to contribute the code but wanted to discuss it first.