The problem with game mechanics trumping RP is that game mechanics are too limiting.
Which, in many cases, is completely intentional. This is, after all, a game that we play for personal enjoyment. A conscious design decision is that you cannot, in most cases, permanently affect someone else's character. Which is why it is
very difficult to kill someone else's character, or do them permanent, debilitating damage.
you should use the most mechanically accurate option available to you to ascertain the desired roleplay results otherwise your just working the system and not your character.
In some ways, yes, I agree with you. This is a decent summation in most respects. (And, really, shows a different interpretation of playing the game that is very interesting.) But along with it, you also have to use the guideline of "If you're using a game mechanic for something other than what it was intended to do, then you're probably doing something wrong". When you use game mechanics, the action itself should speak for itself. If you have to send a message to qualify the intention of the mechanic you're using, then you're probably doing something wrong.
Especially if you have to say something like "I know the game says we're doing X, but we're really just doing Y."
I would also not complain if you roleplayed torturing my character and leaving him mutilated.
You should. That kind of behavior is outside the scope/rules of the game
unless both players have agreed to it. So unless you and the other player have agreed to it before it happens, then the other player has broken the rules. At the very least, he needs to be made aware of the rules before he tries doing it to someone else who doesn't agree to it.