Ok, we'll never know exactly what HIS meaning was for the song so the idea is to leave it up to us. Why not choose the more powerful? It's pointless to debate what happened, just go with the one that makes the song the best to you. For ME, I prefer to say that he killed her, because it adds the effect of an unreliable narrator, and the fact that he was so mixed up with the meaning of "safe." Also, if you use this interpretation, the fact that such prejudice and redicule could drive someone, whether mentally handicapped or not, to kill the ONE thing they love most, REALLY makes you think. THAT'S why you shouldn't make fun of people. :P

Syd

He comes to new town; where he is outkasted (idk why?)
Mary and he were in love! She was his first and only friend there :)
No one gave a sh!t about him (narrator) until the day, mary was found dead.
Fingers pointed, eyebrows raised; he was suspected !

He tries to justify...

Muzic Rocks !!

A boy with a creepy personality and a bad reputation became friends or more with a girl named Mary, who on the surface seemed to fit in a lot better than he did. But in reality she was drawn to him because she hated the place more than he did. They always talked about how, one day they'd escape. One night they met by the river, had a nice long walk. He went home, she ran away. Everybody thinks that the creepy little boy has grown up to be everything they feared; they want answers and there's this one all too easy answer: the crazy boy killed her because that's what crazy boys do. For his part the boy is panicking, thinking that these people have had enough, and they're really going to hang him this time. The local cop lectured him; he said, "I've protected you as much as I can... I can't rescue you again. It's all gone. You're going to have to face up to this."

This boy is a defeated, harried dreamer. His reaction, deep down, is to dream about running off to the river, to follow his one friend to safety.

On a side note: One day I was listening to this sad story, reliving the sadness of being in such a limited world, and the terror of having to answer to the coming inquisition. All of a sudden that name popped up: you see I had fallen in love with a woman named Mary. OMG, I almost had a panic attack. It's almost funny now...