Both my mother and grandmother, both now long passed away, would be horrified if when soaking beans, pulses, barley, lentils or rice etc. overnight for a soup or stew, the soaking liquid was used in the dish itself. My guess is that in their eyes, this action would reduce the amount of scum that floats to the surface during the cooking process, which to my knowledge, appears to be perfectly harmless protein which can be stirred back in.
Looking at similar questions, even the edge case of kidney or black beans, the liquid seems perfectly OK to use, provided it is cooked for the relevant period of time afterwards.
Is there ever a case when one should dispose of the soaking liquid rather than use it as additional flavouring to a stock (which is then cooked for a sufficient period)? Also, if that is not the case, should the pulses be stored in the refrigerator overnight as the liquid will have been stored well outside the safe temperature limits?