Hmm, I would say that him being knocked unconscious would be the best option, but since in the FAQ it said that he's simply held at bay by Hork-Bajir guards, then what is stopping him from morphing? He could either morph something dangerous and risk being killed, or morph a Kafit bird or something without an ear canal that could be infested. But then again he'd either become a nothlit or be killed. Maybe he figures it isn't worth the trouble? (What's a KASS btw?)
Also on that note, I assume that the Yeerks did the same thing once they recieved the morphing technology and began to make morph-capable controllers?