The darkness of man's heart refers to the savage in all of us. Golding is suggesting that society, like these boys, would revert to savagry if left to our own devices. That deep inside of all of us lives the "beast". Golding points it out to us not only through the actios of Jack and his tribe, but also the condescending naval officer who can't believe what they boys are doing to each other (although his job consists of the very same thing).
The end of innocence refers to what these boys will now have to deal with. I always ask my students who they think it would be tougher to be when they get back to civilization: Jack or Ralph. Either way, you have to cope with what has happened on this island, and these boys are no longer going to enjoy the carefree thoughts that most twelve year olds are allowed. They have been a part of something greater and have experienced the darkness of their own hearts much sooner than most.