The dying part is mostly my own fault. Combination of not reading squares correctly (trying to facilitate the fight) and forgetting that ranged attacks provoke attacks of opportunity. I honestly thought I was 15 feet away, but obviously that's not what happened.
Also, as far as the CR is concerned; we're undergeared as well as underleveled. I don't have the +1 or +2 armor the game expects right now, nor do I have a magic weapon.
Rolep, your duel is technically over CR'd, even against mundanes. You fought effectively 6th level PC and 5th level PC, while we're now fighting effectively 11th level NPCs (assuming Warrior, which is only somewhat inferior to Fighter. If they were Fighters, then they'd have Power Attack, Weapon Focus (Claw) and probably Toughness and Improved Toughness; so +1-3 damage per round, no difference to hit, and +9 health, with optionally taking much bigger penalties to hit for bigger damage increase.) Following general NPC - PC thoughts, they're effectively 10th level PCs. They also have 3 attacks, versus the 1 attack your duel opponents had. So each one of these Trolls is triple to quadruple the threat value of the Knights you fought against. You're also not quantifying CR correctly; a PC is supposed to be able to deal with an equal CR opponent once per day (taking 80+% of resources). A Sorcerer or Wizard would probably have been able to deal with a Troll by themselves, but short of encounter-ending spells, nothing else should be able to deal with a Troll in a 1v1 fight at level 6. The DMG contradicts itself repeatedly throughout the book, but Leadership treats PC class followers as 1 level lower than NPC, and for Mundane PC classes, that's pretty fair. I would assume that the DMG tries to CR a PC class as if it had PC gear, rather than NPC gear that they should have.
The whole nonlethal damage thing isn't actually that big of a concern unless the fight lasts more than an hour. We can just treat them as if they had Fast Healing 5. After they're downed, a Coup de Grace kills them.
Edit: Omitted an acronym accidentally.