I had worked on this a while back. Your technique (the one in the previous post, not the one you JUST posted) is exactly what I settled for. (I’m using ATG too).
The permanent solution is to fix the Sonar Runner Gradle plugin to do what you are doing manually. You can fork the Gradle source code and change this file:
String projectPrefix = project.getPath().substring(targetProject.getPath().length()).replace(":", “.”);
should become
String projectPrefix = project.getPath().substring(targetProject.getPath().length()).replace(":", “.”).replace("/", “.”);
I never got around to submitting a patch (the above suggestion is untested) as I couldn’t use Gradle as my build tool because of this problem: http://forums.gradle.org/gradle/topics/is-the-repository-extensibility-design-change-complete
I’m curious how you are using Gradle with ATG, but I guess that’s a question for a different forum.