Hi, fisrt of all, do you need to let the .exe stays opened even it has been stopped? If not, you may wanna try adding "Quit LabVIEW" function (from Application Control) to your diagram to stop/ quit button's true case. This will close the .exe completely.
User will then invoke the .exe from a short-cut on the desktop. (just like any application from your desktop)
For easy editing, you may wanna use [CTRL]+[+]+[.] to stop the program without exiting from labview.
Not sure if this will help.
Cheers