The Torture subdomain's Painful Smite ability says:
Prior to making a melee attack roll, you can choose to convert all damage from that strike into nonlethal damage, adding your Wisdom modifier to the damage. [...]
Say I'm attacking with a greatsword and I want to use this ability. Will I have to take a -4 penalty on the attack roll because I'm using a lethal weapon to deal nonlethal damage?
No, you make the attack roll normally with no -4 penalty because you're not actually making a non-lethal attack. You're using a Lethal weapon to cause Lethal damage, this Supernatural ability converts all of that lethal damage into Non-Lethal Damage = to your Lethal damage + your Wis Mod and gives you a free Intimidate check, and then use this entire amount of non-lethal damage caused as a bonus to this Intimidate check.
Happy to hear that, thanks!
Slightly off topic but would the distinction between nonlethal and lethal even matter in this case? I mean, say you wanted to lethal damage rather than nonlethal damage. The only difference is that the nonlethal damage would cause the enemy to fall unconscious rather than die, but at that point you can just walk up to them and kill them after the fight anyway, right?
So, really, the fact that you're dealing nonlethal damage seems like an additional perk of this ability, seeing as how you can easily "convert" it back to lethal damage retroactively by simply doing a coup de grace on the unconscious target.
Yes, causing non-lethal damage can be very strategic, because sometimes you don't want to kill the guy so you can interrogate them afterwards, or if you have an ability that can cause a lot more non-lethal damage than you would be able to cause lethal damage, such as with Sap Adept/Master or Painful Smite, and drop them to unconscious so you can move onto another threat quicker, or simply because you think you can drop them unconscious with a massive non-lethal hit and then coups de grace them because it's quicker. There are plenty of good reasons to use non-lethal.
The main problem with causing non-lethal damage is that it's easily healed.
You heal nonlethal damage at the rate of 1 hit point per hour per character level. When a spell or ability cures hit point damage, it also removes an equal amount of nonlethal damage.
So if your enemies have a healer of some kind, and he heals a person for 20 lethal damage, he'll also heal them for 20 non-lethal damage. So if you expect your enemy to get healed, you probably don't want to cause non-lethal damage.
First of, full agree with Ryze Kuja: No -4 penalty.
Slightly off topic but would the distinction between nonlethal and lethal even matter in this case?
Constructs and undead are immune to nonlethal damage. There's also some abilities that protect against non-lethal damage, e.g. Invulnerable Rager Barbarian's Invulnerability or the Mummification Alchemist discovery.