The Prime Barrier is a part of the physiological makeup of Homo superior that prevents them from deliberately killing a living thing.
Ultra's Anax Project allowed John Young and Killian McCrane to overcome the Prime Barrier, granting them the ability to kill. John being the truly successful outcome of the project, as it made Killian insane. 
In "Limbo", a Tomorrow Person named Michael turns out to be a serial rapist. He beats Stephen unconscious, then throws him into a sewer. This shows that the Prime Barrier only extends to the deliberate taking of a life, and does not prevent causing physical or mental harm, nor actions that indirectly result in death.