Billions? Where did you get billions? Morpheus clearly implies there are only 250,000 people in Zion. As he says the 250,000 Sentinels coming in are "machine thinking" of one for every "man, woman, and child" of Zion.
He's talking about the people inside the Matrix. I heard from someone that games are planned to go on after the events of the movies, like a MMORPG or something. My guess is allong his lines: yeah, you defeated the machines, but if you just shut down the Matrix, the billions of people connected couldn't last off the resouces Zion can provide, plus many wouldn't enjoy leaving that comfortable world for the real post-appocalypic one. So they turn off the human-farms, but leave on the Matrix, slowly waking the people up that they can.