I strongly disagree. Not only does the voice of God not sound anything like Mr. Jones, but the actor doing the voice uses a British accent, and I've never heard Mr. Jones do that.
On my most recent re-watching of the film, I finally realized (after who knows how many viewings over the past 10-plus years) that it is Ben Kingsley doing the voice of God. He seems to be using a different voice than he uses for Moses, maybe even a slightly different accent, and I'm sure that they manipulated it in some way, but the more I listen to it, the more obvious it is that it's Mr. Kingsley. Maybe it comes from seeing (and hearing) him in so many other things since then.