Any sensitive information at the app level (application.json) can be protected by using:
{ "settings": ["runtime:server"], "secret": "xxxx" }
that group will never be sent to the client side.
In the other hand, if you want to keep a secret at the mojit level, your best choice it to add it to definition.json for a mojito with controller marked as "server" affinity. You might also use "runtime:server" on definition.json if you have a client side affinity in the controller. I don't think we have tests for this use-case, test it, and let us know.