Are you sure you are turning off WM Assistant? It is not enough to just click the Home button on the iPhone, because although the WM app is cleared from the screen, it is still active and working in the background. Double-Click the iPhone Home button to display all active apps at the bottom of the screen. Push and hold one of them until the small cross appears in the top right corner of all the icons and then close the apps by touching the cross.
I close active apps several times a day to save wasting the iPhone battery.
The previous WM Assistant had a red slider to activate and deactivate. The 5.24 version does not have it - or if it does I have missed it. You may actually be right about the ability to adjust gains etc whilst airborne but personally, I would feel uncomfortable with that and prefer to land, change the gain, and take off again. Too easy to scroll to something disastrous.