Looks like currently there is no way to disable/remove debug code with Google Closure Compiler API usage, since it doesn't support define flag described here - https://developers.google.com/closure/compiler/docs/js-for-compiler (look for ENABLE_DEBUG variable).
The wiki (https://github.com/google/closure-compiler/wiki/Additional-Webservice-Options) doesn't clarify what is the purpose of debug flag there, but looks like it has some other meaning or not supported by API.