This is effectively the same paradox some friends and I discussed in college. Another way of looking at it is:

If you connect an ideal voltage source through a resistor R to a capacitor C, the amount of energy required to charge the capacitor is CV^2 while the amount of energy that winds up in the charged capacitor is 1/2 CV^2. The other 1/2 CV^s is dissipated across R. This is unaffected by the value of R, even as R -> 0. The only thing that changes is the charge time.

R = 0 is impossible for real circuits, but no matter how close you get you still lose half of that energy in the resistor.