Even though they're supposed to think on their own, you should still be able to give them directions. Limited directions such as don't attack a certain target, or attack a certain target, or heal me... and so on.
After all, they're on your payroll. You should be able to tell them what you want or don't want them to do.
Maybe they wouldn't always do what you said (random chance to ignore you?) but you should still be able to give those directions and have a good chance they'd follow through.
Minions should be the same way except no random chance to disobey you. They're not hired, you own them (well mostly) and they should be the little, loyal minion that does everything master says.
I'm thinking that maybe there could be an option to click on a Henchman or Minion's name in battle (on the piece of paper like thing on the screen that also shows health and pips) and select from several options kind of like menu chat.
Great idea, I've wanted this to happen for so long! I don't think that we'd be allowed to click on the minion every round though, so maybe we have a limited number or every couple rounds we can? Well, I hope this plays out in the game someday. :-o Thanks!