how can I disconnect proto-repl so that I can close atom and reopen atom and restart proto-repl

When you close Atom, the REPL will disconnect -- perhaps I'm not understanding what you are asking @hotbelgo?

Otherwise ctrl-alt-, e will stop the REPL.

It's the Proto Repl: Exit Repl command. Also bound to ctrl-, e according to the command palette.

Cool - thanks @seancorfield - its felt like closing atom was not sufficient sometimes, but perhaps it was some other beginner problem that was actually to blame

The other useful command is Proto Repl: Interrupt bound to ctrl-shift-c.