Kabutops is another Poke that beats RotoFable, it's a generally weak combo against rain teams in general(though Clefable can attempt Twave Sboiled stall on special attackers).
Something like a SubPunching Cacturne works well too.
Really in general this combination isn't that hard to beat, especially on the physical side. If your STAB move can hit Rotom super effective or neutral than Rotom goes down pretty easily and you will also take down Clefable. Non-STAB Ghost or Dark moves can also take down Rotom, though these are somewhat rare.
Something like a SubPunching Cacturne works well too.
Really in general this combination isn't that hard to beat, especially on the physical side. If your STAB move can hit Rotom super effective or neutral than Rotom goes down pretty easily and you will also take down Clefable. Non-STAB Ghost or Dark moves can also take down Rotom, though these are somewhat rare.