You can register your mock and inject it instead of the original service.
application.register('service:mockLogger', mockLogger, {
instantiate: false
});
application.inject('route', 'loggerService', 'service:mockLogger');
application.inject('controller', 'loggerService', 'service:mockLogger');
I use this approach for mocking the torii
library in my third-party login acceptance tests. I hope there will be a nicer solution in the future.