The Atom editor is a very good product, but in some areas it attempts to deviate from long standing user interface standards for operating systems, which can extremely annoying.
For example, on a Mac running OS/X, all apps compliant with Apple's guidelines will handle a Copy command with no selection by leaving the clipboard intact. On Atom, this action will either delete the contents of the clipboard if the line is empty, or overwrite them with the contents of the entire line.
Deviating from such very basic user interface guidelines is not a good idea, but if it's going to be done, the deviation should be an option, not the default.
Is there a way to force Atom to behave the way it should on a Mac, through options or scripting?
Figured it out.
Adding the following at the bottom of the keymap.cson configuration file returned Cmd-C to the correct behavior.
To edit the keymap.cson file open Preferences, then Keybindings, then click on "your keymap file" at the end of the sentence under the "Keybindings" title.