I would say that it depends on what the criminal is doing at the time. There are a lot of things that could make me think they would still be an imminent threat, making the answer of yes, I am willing to destroy him. If he is still holding or is near enough to grab something that could be used as a weapon, or has hands hidden, or is even moving/twitching in a manner that indicates he might snap/attack. Or, even if he is perfectly still, but you can see in his eyes that he has not surrendered or given up, but is waiting for an opportunity to attack, I will most definitly be keeping the gun pointed at him.
I would say if they are cooperating and no longer suspicious, and this is the most important part, I am able to be a safe enough distance away that I know I could reaquire the target before he got to me, then I would shift to a low ready hold. In my house, several of the rooms would not allow me that safe distance. I will not allow an intruder the oportunity to take my gun away and then harm my family or myself.
So after the long answer, the short answer is yes, I think pointing a gun at a bad guy is an acceptable "violation" of the safety rules, because I don't think it is a violation in the proper circumstances.