The testing, and perhaps even the specific methods of the this test, are not the question. The question is the morality of CMU being paid by authorities to uncover PII about hidden services and report back to them.
Test the system (potentially with your own uni's red/blue teams instead of on other 'public' hidden services) and report back anonymized reports of the data. One can say "Doing X, I got result Y" without giving out the personal details of results, much less to the FBI.