Turn Popups On/Off in ArcGIS Online Webmap via Javascript API Web Application

Think you almost have it. It may be that you need to reset the handle on connect...

clickHandle = dojo.connect(map, "onClick", clickListener);

The following is working for me...

var agolPopupClickHandle,
    agolPopupclickEventListener;

    //get the response
    .then {
        agolPopupClickHandle = response.clickEventHandle;
        agolPopupclickEventListener = response.clickEventListener;
    }

    //connect editor
    if (agolPopupClickHandle) {
        dojo.disconnect(agolPopupClickHandle);
        agolPopupClickHandle = null;
    }

    //disconnect editor
    if (!agolPopupClickHandle) {
        agolPopupClickHandle = dojo.connect(theMap, "onClick", agolPopupclickEventListener);
    }

So with further trial and error, I discovered the issue. I was unaware of how dojo.disconnect and dojo.connect work.

If I turn off the ignorePopups option when calling esri.arcgis.utils.createMap I will get the standard popup. Then, in the mapDeferred.then call, I set global variables

clickHandle = response.clickEventHandle
clickListener = response.clickEventListener

Later in my initEditor function, if bool == true then I disconnect clickHandle

dojo.disconnect(clickHandle)

In the else clause:

dojo.disconnect(clickHandle)  // This will disconnect the original clickHandle if it is still connected
clickHandle = dojo.connect(map, "onClick", clickListener)  // This will reconnect clickListener and return a new clickHandle that can be disconnected next time the editor is enabled

The issue was that I had multiple handles connected to the onClick event and I was only disconnecting one or the other and not both.