How different are the films from the comics?
Considerably. For instance in the comics Duke is a First Sergeant whilst in the film he is a Captain. Cobra Commander himself never knew Duke, was never a maimed soldier but a car salesman who turned against America after the failure of his business and death of his brother in the Vietnam War (in the British-Action Force backstory he was Marcus Kassels, the disgraced son of an aristocratic Swiss diplomat and
scientific genius who served in the British Army and led a US platoon nicknamed 'The Baron's Brigade' in the Korean War before being accused of a massacre of civilians. He fled to Africa where he became a mercenary, fighting in conflicts all over the world before forming his own private terrorist army, the Red Shadows and adopting the alias Baron Ironblood, based on his family's Latin motto of 'Sanguineo Ferris'-our blood is of iron. After numerous defeats at the hands of Action Force he would abandon the Red Shadows and form the Cobra organisation, adopting the new identity of Cobra Commander).
What are the differences between the Theatrical Version and the Extended Version?
The "Extended Action Cut" is quite well named with this title because it is substantially better than the theatrical version - not only in the action department. A number of more violent moments are back, a few large ones that are completely new and surprisingly much more character development that even leads to some minor changes in the story. While American audiences will have to be patient to get their hands on the Extended Cut (it is Best Buy-exclusive for the first weeks), British customers have it easier. All Blu-ray editions feature both the theatrical and the Extended Cut. In total the Extended Cut runs approx. 12 minutes longer than the well-known Theatrical Version and a detailed comparison between both versions with pictures can be found here.
So all the characters from G.I. Joe: The Rise Of Cobra are dead?
The entire question is left deliberately vague. We are told that both the GI Joes in the field and at their base have been wiped out with the exception of Snake Eyes, Roadblock, Lady Jaye and Flint. However we never see it and it is perfectly possible that any of the characters may have survived in the same way that the main characters in this film did or simply left GI Joe in between this film and its' predecessor. The only character we know to be dead for sure is Duke whom we know is killed in the desert attack.