James H. Schmitz's story "Puvyq bs gur Tbqf" (nearest link available; click "Contents" in upper right) has basically this situation as well; in fact, it's the climax and resolution of the whole story, so I've rot13'd the title. Here the 'masters' did not fail, and in fact arguably got the best result they could have under the circumstances, and yet autonomy is still restored at the end, and the whole thing is logically sound.