Sherlock hates Magnussen. He just loathes him and his character with all his being.

Quote:"Well, I am afraid I can't help you, Lestrade," said Holmes. "The fact is that I knew this fellow Milverton, that I considered him one of the most dangerous men in London, and that I think there are certain crimes which the law cannot touch, and which therefore, to some extent, justify private revenge. No, it's no use arguing. I have made up my mind. My sympathies are with the criminals rather than with the victim, and I will not handle this case."

Gatiss and Moffat have stated that they believe it's a possibility that in the original story, Holmes was the one who had killed Milverton, and Watson had covered it up in his retelling of the case.

The plan was with the laptop at Magnussen's location, Mycroft would bring his men and raid Appledore, having access to the vault without all the diplomacy of needing a proper warrant. Since the vault didn't exist, Magnussen would be able to implicate Sherlock and Watson in selling state secrets, which would bring Mycroft under his thumb as his pressure point is Sherlock. Up until the very moment he revealed that all his information was stored in his mind palace, the assumption everyone had was he had a backup plan, which is why he was never killed, or taken away by the government.

Magnussen didn't have a backup plan because backup plans are for villains. It was never in his realm of possibility that he would actually be murdered, much less by John Watson or Sherlock Holmes. He saw himself as a businessman. He saw himself having complete control over everyone. He didn't fear death because he never thought it was a possibility, with the grip he held on others. Mary might have killed him if Sherlock didn't step in, or he may have wiggled his way out of it with fake promises and lies, playing that the gun is a bluff. She wouldn't necessarily know he didn't have a backup plan. That's what she was there to find out. How much he knew and how she could make him stop, even if it meant killing him. In Magnussen's eyes though, he probably saw her like everyone else, with a price or a pressure point, and he would have played at that.

Sherlock waited for the police helicopters because Magnussen had armed guards inside his home. Mycroft would tell the police to hold fire. The police would prevent any guards from shooting on Sherlock. The solution is that Magnussen had to die.