How about making this a single RigidBody with either a single mesh consisting of two balls or two ball meshes. Plus two collision shapes. You can make it rotate via the add_torque method.
It will get more complicated if you actually want two separate rigid bodies. In that case you would use one or more rigidbodies between the balls which are joined with joints. (Emulating some kind of rope/chain).
A completely other way would be to do physics on your own and use kineticbodies instead.