I think the point is that the zero point of the energy diagram is set arbitrarily. They could have just as easily selected the zero of energy to be at the lowest energy point of the energy curve, so that any excited state was at a positive energy and there could be no negative energy values.
The point of selecting infinite separation is that it avoids any energetic interactions with other particles, therefore it is really the energy of a lone electron and a lone nucleus.
It makes sense to have some meaningful zero-point for the energy because it allows for comparrison of the energy as the electron approaches very close to the nucleus (energy starts to go up fast, and is eventually higher than the zero-point energy). I think that this can also explain how electrons can reach excited states that are high enough in energy to allow for loss of the electron; all you would need, theoretically, is a positive energy.