I think the problem with the spinning elbow JJ did to Bonnar was how it was set up.
Yes, it clearly hit him in the back of the head, no doubt about it, but when you're in a fight and the combatants are facing each other (or close to it), that elbow would end up being a clean strike to the jaw or side of the head. As soon as the fighter whose trying to defend against it move/turns his head/ducks, etc it's more likely to make it an illegal blow. The fighter attacking with a single strike, can't be held responsible when the fighter defending moves into a bad position.
It's like when a fighter is down and covering up, but turns his head in such a way that a legal strike becomes illegal and hits the back of the head. A single shot isn't really frowned upon, it's the followups that get people in trouble.
I'm not a JJ fan by anymeans, but that particular strike has never bothered me.
As for the kicks, I also don't really see the problem. I've been training MT for about 7 years and have run into a ton of guys that could severly damage a knee with a kick to the side of it. That's why you have to learn to defend it and check the kick. It's the same with the straight kick to the knee, you can check it in a similar fashion by just raising your leg a bit and taking your weight off it.