The developers of the Atom editor decided not to make code folding easily configurable.

To turn it off, add this to init.coffee:

# Disable code folding
{TextEditor} = require('atom')
TextEditor.prototype.isFoldableAtBufferRow = -> false

To disable the large, empty margin, edit styles.less:

// Disable code folding margin
atom-text-editor::shadow .gutter .line-number .icon-right {
  display: none;
}