Some loopers have a fade-out function, which can be handy. I agree, a full fade is pretty weird live, but you can also combine it with Larry's technique, play in unison with loop, start the fade and keep playing. Fade a bit, then kill the loop. That will make the drop in volume (maybe) a bit less obvious. May not work everywhere, but it's one more trick to have up your sleeve as long as you have a looper that can fade out.
BTW, I do several examples of stopping a loop, while hopefully creating a somewhat natural ending by continuing to play in real time as the loop ends in the article I did for AG on looping recently: (Also, for those interested in ToneDexter, it got some use in this video as well)
http://acousticguitar.com/a-guide-to...w-to-use-them/