I kinda think the rule about hunters killing Men of Letters is probably something they see very much like the idea of putting down a dog that's turned on its master, unfortunately. Dr. Hess even specifically said that hunters are dogs. They're supposed to be obedient and loyal. If they've killed a Man of Letters, it sounds like they see them as irredeemable.

However, Toni's assistant seemed like she was probably more of a hunter than a Woman of Letters, which would mean that it would just be considered hunter on hunter violence.

Also, Toni was acting against the wishes of her superiors. She defied orders and sent her assistant to attack them. They were forced to defend themselves. I kinda feel like it's possible that might have voided the rule about hunters killing MoL in that particular instance, too.