I teach at Western. I know academic freedom well. Academic freedom requires an environment of enabled autonomy with researchers free from undue external influence. State military actors are undue influencers, whether academics like to admit it or not.
There are limitations on what can and should be done in the name of academic freedom. Just as a researcher is not permitted to falsify research or plagiarise, they should not be able to aid and abet foreign military actors at the risk of Canada's national security.