Equip Kylie with stuff that raises her hacking odds. Also, if you can't take them over just try to shut them down or confuse them, those odds are always better and still quite useful.
If you must fight them without tricks, try to engage them without too much distraction from other enemies and just pile on the damage as quickly as possible. If you can get some expendable cannon fodder (pets, drones, confusion protocol, hacked regular bots, mind-controlled enemies) while you DPS them, all the better. Even if the Destron takes them out in one turn, that's still one turn you're not losing your own characters.
I managed to deal with the three special Destrons in the final Violent Case by letting Bianca mind-control Ben and some of his goons and having them engage the Destrons while my team piled on the damage from a distance. High-damage single-target attacks work reasonably well against them, I think Heixing's Annihilation Shot did the best damage of everything I threw against them.