Typically the whining isn't a "bad" sign. Most electronics whine/vibrate, just mostly at frequencies above what we can hear. Unfortunately sometimes you get PSUs, Video cards, or Motherboards that produce that annoying whine noise. However, the only bad thing about that noise is how annoying it is.
There are things you can do to reduce/eliminate the whine. For example sometimes gluing down the part that is whining can help, but this is a task not to be taken lightly. Usually this is done with capacitors, not VRMs that can get hot.
Sometimes the whining can be caused by other things in the house. For example, in the house I am renting there is an old dimmer switch in the kitchen paired with new fluorescent bulbs. Whenever this light is on and my computer is drawing more than idle power there is a buzzing noise coming from my PSU. Annoying? Definitely. Dangerous, nope.
Also, the motherboard is whining, but it might not be the motherboard's fault. If you have any spare PSUs you might try swapping just to double check and see if the whining remains.