I think it's possible that he hired Cloane -- but long ago, i.e., in Season 2 as part of the whole "gaslighting" thing. He would've needed a double for the Alliance to go after, as he didn't know how long it would be before Syd and Jack brought down SD-6. So he hired this guy, gave him all the information he'd ever need to BE him, introduced him to Rambaldi -- and then realized too late he'd created a monster.

Now that's a brilliant idea and would be such a Sloane-ish thing to do. It would also explain why he doesn't seem to be really surprised there is a doppelganger out there on the one hand, but genuinenly disquieted on the other in the scene when Sydney comes to him after having seen the guy.