Lex has reasons for wanting absolute mental control over his soldiers. Partly because of meteor psychosis - most mutants have fairly evident neurological problems; combining all those powers couldn't be good for the brain. The soldiers might well be functionally insane without the mind control.

Also, if the alien defense hypothesis holds - Lex knows the aliens can take over peoples' minds/bodies. Zod took him over, and Lionel was possessed by Jor-El. So soldiers operating on remote control might be the only reasonable option.

Your theories always click with me -- I get this great 'Of course!' moment, with the proverbial light bulb flipping on in my head. Mind-controlling the supersoldiers to prevent violent insanity and/or alien mind-control makes perfect sense! So Lex still isn't totally evil; he isn't doing this just for sick kicks. He's being extra-careful to keep his troops on the side of humanity, as opposed to letting them fall into chaos or the enemy's hands.