Think about it...
"Murdoc is God
Murdoc is dead..."
If Murdoc is metaphorically both God and Dead, then that means God is Dead. It's a song about losing faith in religion.
Also, Murdoc is an important symbol for Atheism, as he is a Satanist. True Satanists are essentially Athiests or Agnostics. They do not actually worship Satan. Satan to them is more of a force of Nature, like Karma or Luck.
Obviously, the hard rock sound is representative of Murdoc's musical influences.
Not sure about the whole Johnny thing. I'll have to riddle that out.