The first rule of a serious conflict is this: survive it, if you can't avoid it.
If you did what you reasonably could have done to prevent the confrontation from degenerating into a melee, then it's probably serious enough that the other guy would be out to cause some serious harm to you. If it's that serious, then you had better not pull any punches, since your first goal is to survive. You should use whatever you have at your access, to stop the other guy. If the fight is over after you've applied the force, then so be it. Don't continue it, of course, since the guy is no longer a threat.
Please note, that while I do advocate using your best techniques to survive the encounter, this does NOT mean that you should attempt to break the guy's neck if you have the upper hand! Breaking an arm, leg, etc, though, shouldn't come in the way of you surviving the fight.
It's the same thing I'll tell other people when it comes to firearms; you don't shoot to scare or wound; you shoot to stop the other guy. If you manage to incapacitate him with a shot that happened to just wound him, then it's over. Don't continue on, if he does not present a threat anymore.