Sorry I didn't see this in my original search, but this thread actually covers what I was talking about, How do I disable mouse look when a button is pressed? Maybe my mis-phrasing will help some other hillbilly find his answer too...

You check the current mouse position against the window containing your GUI element(s) and set a global (I use a Plugin, you could also use a common script object). Then in MouseLook, return early from Update if that's set. Also, clear that global boolean in a LateUpdate function.

I made this my 'global' variable manager:

using UnityEngine;

public class GUIManager : MonoBehaviour
{
    public static bool GUI_is_showing = false;

    public static void SetGUIShowing (bool val)
    {
        GUI_is_showing = val;
    }

    public static bool isGUIshowing()
    {
        return GUI_is_showing;
    }

    void LateUpdate()
    {
        GUIManager.GUI_is_showing = false;
    }
}

Then in my OnGUI() functions:

windowRect = GUILayout.Window (1, windowRect, EditView, "My View"); 
var mouseOverMe : boolean = windowRect.Contains(Event.current.mousePosition);
if (mouseOverMe)
    GUIManager.SetGUIShowing (true);

Then in MouseLook:

void Update ()
{
    if (GUIManager.isGUIshowing())
        return;