The Intex SWG is not certified as safe while swimmers are in the pool because either the design is flawed or Intex didn't bother with the certifications - they cost money to get. That being said, I think any danger is minimal so long as a) everything is properly bonded (including the water) and b) the SWG is plugged into a properly grounded GFCI. We swam all last summer with an Intex SWG that ran while we were swimming. The first I heard of this was reading a different thread 5 minutes before writing this post. Plus, the SWG does have some power to it even when it is not active, because it is in sleep mode. So to be perfectly safe you'd have to unplug it each time you swam. At least the Intex one I have that means reprogramming it each time it is unplugged.
My manual doesn't say anything about not swimming while the SWG is running.