First of all, Ocelot himself scoffs at the idea of witchcraft and the supernatural. Wouldn't you agree that that's a bit of a strange thing to say when you're periodically being possessed by the ghost of your dead boss? Unless of course, you know something the audience doesn't. (the most common answer I get to this is that seconds after his speech Fortune deflects some missiles to which my reply is always the same; Is it more likely that Fortune, by some massive coincidence, does in fact possess the mystical powers that the Patriots tricked her into believing she had, OR is it not more likey that someone other than Ocelot; GW, another Patriot agent, Ocelot, Olga or a million other possible suspects simply turned on her EM field generator again, unbeknownst to Ocelot?).
Then there's the fact that, as far as I recall, Kojima was pretty widely quoted as saying that an explanation about Liquid/Ocelot would be forthcoming in a sequel, and he said this shortly after MGS2 was released. Put simply, I don't think the spirit medium explanation was ever meant to be the correct one. I don't think Kojima knew what the explanation would be, but I'm pretty confident that he knew what it wasn't.