1) Why don't the prawns help Christopher and Wikus during the big battle at the end?
Because they were being moved to district 10
2) When Christopher and Wikus assault the MNU building, Wikus is seeing getting security access using his codes and fingerprints. Wouldn't the MNU have already deleted him from their database after being a fugitive?
It was less than day and he was going to be killed, probably not the top of the agenda. or call it artistic licence.
3) Why does only Christopher want to gather fluid to get off Earth? Why don't the rest of the prawns help him?
They make a clear point that most of them were stupid workers and that christopher was one of the only intelligent 'prawns' which is why he that set up and the other 'prawns' didnt understand what he was doing.
3) How does Wikus start the car on the getaway from the MNU complex?
either call artistic licence into play or he hotwired it.
5) When Wikus is piloting the hidden shuttle, he is shot down by a Surface to Air Missle (SAM) unit from the MNU. At the end, however, when Christopher and his son use the hidden shuttle to fly back to the mothership, why don't they just shoot them down again?
One assumes because the south ifricans were so happy to see them leaving.