They were sort of possessed so he had to kill them. Ok, he didn't have to kill them, he could of snuck around.

Think about it, if your parents were possessed and the only way to save them was to kill them would you do it? Like the people of Hyrule. Link had to save them and he had to kill innocent victims (guards) to get into the Dark World, kill Ganon and get the Triforce to save the people of Hyrule.