Pull the other one. It may be empty of matter, but there is something there. Otherwise, we'd have matter coming out the wazzoo, since most of the universe we can inspect is "empty space"(devoid of matter). I know of virtual particles and particle pair production. But you have to have other things around for matter to be produced.
And that negative gravitational energy, I think is called "potential energy". The same principle applies to the positron and electron. The charges on those particles produces an attraction which is called potential energy until we allow the particles to move closer together. Then it becomes kinetic energy. However, unlike two massive uncharged bodies, the electron-positron pair gives a bit more energy than the potential/kinetic energy when they get close enough. They annihilate.
Plus. one other factor, photons have no mass. They have energy. So what offsets the energy tied up in the photons?(speaking of a zero energy universe)
I did find another quote from a physicist to the effect that "The reason that there is Something rather than Nothing is that Nothing is unstable." Cool, huh?