Well I feel like this, pistol whipping someone to knock them out isn't the same as beating someone to death with night stick. I understand nonlethal damge isn't a thing per se, but choosing to not kill someone when delivering the killing blow is kind of the definition of nonlethal damage. And again, rogues don't fight like warriors, where it's straight up weapon and attribute damage. A fighter choosing to hit someone with the broad side of his sword and do the same damage as him slashing is understandable, but a rogue trying to use sneak dice to do the same thing is not. The simplified rules create holes, like for another example, you can't choose to not kill someone with a ranged or thrown attack, but if someone wanted to keep someone alive, could aim for non-vital areas like a leg or arm. Or they can shoot them with a practice arrow.
The reason I asked for the opinion of other DMs, is because as a DM we are allow to change the rules, or circumstances of an action, a player is not; and I like to do that. If something doesn't make sense in the rules, or for a situation, I won't hesitate to change it.
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Absolutely - you should customize these rules for your players and your own desires. In fact, you mentioning the ranged attack thing - that's a rule I've ignored for so long I had completely forgotten about it haha. Just like you said, if my players want to take someone alive, I have no problem with the archer doing it with a well-aimed shot to a non-vital area.
A rule I use with my older game group (I've had it since the early 90s), is that to 'pull your punch' you have to declare it before the attack, and depending on the weapon type, you have to wield it like an Improvised Weapon. In example, you may be trained to slash with a scimitar, but you're definitely not going to use that same training to bang into the back of someone's head. With that in mind, I use the 'bloodied' rules from 4e so my players have a rough estimate of when a creature is falling. If they want to take the foe alive, they'll have to roll without proficiency, and drop the damage dice (1d4 for one-handed, and I do 1d6 for two-handed improvised) to pommel strike. Alternatively, I give the bad guy 'Superior Cover' for ranged attackers trying to take them alive, representing the accuracy difficulty of a 'called shot.'
That could possibly be something you use to help you alleviate the sneak attack issue you're having. I personally don't really have an issue with Sneak Attack doing 'non-lethal' because most of the time, we play a very goodly group and my rogues like re-flavoring their sneak attack away from 'ambush' and more toward 'finding an opening', especially since you can get that extra damage just from having an ally adjacent to your target. Like in reality, how something hurts a lot worse when you aren't expecting it - step on a lego bare-foot and had no idea legos were on the floor, just always seems to hurt worse than when you're trying to avoid them, but screw up. *glares at son's bedroom floor*
So long-post-short, you're definitely in the right to make it make sense for you and your group. I don't have a similar issue with sneak attack, but making the player declare it before the blow is struck is a good start. For ramifications, you could say that if the rogue is trying to 'sap' the target, but fails to deliver enough damage to knock the foe out, it only does half damage instead. Could make for some interesting strategy.