Connecting USB shield to system ground
So the question here is: How should I connect the receptacle's ground
  to the circuit ground to avoid this issue and stay clear of EMI
  issues?


A good reason that I can think of why a USB shield is not galvanically connected to ground is because a USB port can be expected to survive EN 61000-4-5 indirect lightning surges and, when testing is applied, the shield is connected to the surge generator via a 2 ohm resistor. So, if the surge level to pass is 2 kV, the peak current that can flow through a grounded shield is about 2,000 amps.

What I have seen something like this: -



And the capacitor is usually rated around 1 kV. On Ethernet cables it's more common to see a 2.2 nF or 1 nF capacitor rated at 1 kV or more.