Mary

They say that the song is about a certain Mary: Martha's and Lazarus' sister. Maria and Martha pledged for the resuscitation of Lazarus. A miracle like this wipes hesitations about whether or not Jesus is the Messiah or only a prophet. If so, the song is a religious statement.

But she is not the only Mary in the Bible. Maybe she is Maria Magdalena: this Mary cries for the lost of the one who, by means of compassion, sees his humanity in the human drama of the other. If so, the song is about the human seed fostered by the heart.

She could be, nevertheless, a third Mary: the one who cleaned Jesus feet with balm and wipped them with her hair. She cried of joy for the forgiveness of her sins. If so, the song is about hope.

Maybe they were the same woman...

I think, however, that weeping Mary is the sinner one. And only the sinner. The liberty will free the bodies of the slaves, like other bodies were liberated from the Pharaoh. Whereas the grace of God will embrace the faithful souls: no matter if they sinned. There's no reason to cry, there's hope, even if you feel like a feather in the air.