All of the T4 training, which trains punisher effectiveness/specialty, must be the first training action, so you can't do an Obedience training first. Unless you're training the CON punisher, of course, since Drain Soul is an Obedience training they won't be able to resist that one, ever.
Yeah, standard chosen only go up a few % per PLEA level for Hypnosis. So what you do depends a lot on how much EE you have to throw at the problem.
The EE efficient solution is 6 turns, 3 captures, basic commander, costing 14EE. Capture each one as they come in. Try to find an initial Chosen that doesn't have any allies coming in on Turn 7 so you can Capture each one as they come in. Set up the three for an Orgy, but don't take it. Use whatever Defiler moves you want on the Chosen, until you know the next one to break free will put Extermination over the top. When your Extermination is about to fill up next time a Chosen breaks free, Inseminate whatever Chosen has the least turns remaining and Force+ the other two. When the first Chosen breaks out, let her be free to use moves until the other two are one turn away from breaking out, then Surround her and let the other two do moves. Each time, when there's one turn remaining on a Surrounded Chosen, Surround the next one in line and Force her. Don't even try this if you don't have Networked Consciousness.
If you've got more EE to throw at the problem, use 5 captures and Flight on this basic commander, costing 54 EE, which means you're spending down your EE slightly if you're getting 45EE/day. You play this one just as above with your first three captures, but then once they're all flying, you can Capture two of them in sequence to make sure that each of them uses Fantasize on each stat (4x per Chosen). This plays out like the last one, but better. Use this if you're getting 45EE per turn at least and have Passion Release and Soul Resonance. Both of these methods use a basic Commander to avoid the Chosen using Self Destruct.
If you've got even more EE to throw at the problem because you're getting 150EE/day, use one with PLEA Punisher, INJU/EXPO Defiler, HATE Suppressor. 4-5 turns and 5 captures, for 106-108EE. You want to be able to Surround each of them after your Commander gets through with them. As before you'll Force+ the last two to break free and Inseminate the one that will put your Extermination% over the top when she breaks out. You can only create this Commander with Completion, an endgame upgrade.