First, the Enterprise (or any other starship) when in orbit is usually in a geosynchronous one so the motion of the planet, the orbit around it's sun, etc... are irrelevant when talking about transporters.
Second, How does Kirk know if Nero still had any weapons available? He gave him an option (which may or may not be feasible, but he gave it to him none the less) , Nero recited all the things he'd rather do than be rescued by Kirk (et al). Nero seemed like the type that would go down fighting. Kirk doesn't know if there were any weapons left, transporters operational or whatever. The Nero/Kruge analogy is valid. Offered to be saved, counter-offer of trying to kill Kirk (Nero still may have had that option), Kirk has had enough.
Where do you get the idea that the ship is in geosynchronous orbit? The Enterprise was very close to the planet. Assuming Vulcan doesn't have a 2-4 hour day the ship was in a standard orbit.
Terminal velocity on Earth is about 195 km/h. Vulcan has a thinner atmosphere and stronger gravity so it'll be a bit more but still in that general neighborhood. Let's assume it's about 50% greater. Are you saying that every time we've seen someone transported the ship had to be hovering over them with the difference in their respective velocities was less than 300 km/h?
The difference was that Kruge waas activly trying to pull Kirk over the cliff. Nero's ship was in the process of being eaten by a black hole. No weapons were being fired. No indication that weapons were being charged. Kirk executed a man who was no longer a threat. Should the solders who found Saddam Hussein have just decided to execute him on the spot? No, they took him into custody and turned him over to the authorities for trial. It doesn't matter what the scale of the crime is. You capture, you put on trial, you pronounce sentence. He should have been turned over to the Vulcans for trial. They are the injured party. It's their right and responsibility.
Judge, Jury and executioner combined with the planet destroying power of a starship is a very dangerous combination.