A vortex molecule is a topological excitation in two coherently coupled superfluids consisting of a vortex in each superfluid connected by a domain wall of the relative phase, also known as a Josephson vortex. We investigate the dynamics of this excitation in a quasi-two-dimensional geometry with slab or channel boundary conditions using an extended point vortex framework complemented by Gross-Pitaevskii simulations. Apart from translational motion along the channel, the vortex molecule is found to exhibit intriguing internal dynamics including rotation and rotational-pendulum-like dynamics. Trajectories leading to a boundary-induced break-up of the vortex molecule are also described qualitatively by the simplified model. We classify the stable and unstable fixed points as well as separatrices that characterize the vortex molecule dynamics.