We numerically demonstrate and characterize the emergence of distinct dynamical regimes of a finite temperature bosonic superfluid in an elongated Josephson junction generated by a thin Gaussian barrier over the entire temperature range where a well-formed condensate can be clearly identified. Although the dissipation arising from the coupling of the superfluid to the dynamical thermal cloud increases with increasing temperature as expected, the importance of this mechanism is found to depend on two physical parameters associated (i) with the initial chemical potential difference, compared to some characteristic value, and (ii) the ratio of the thermal energy to the barrier amplitude. The former determines whether the superfluid Josephson dynamics are dominated by gradually damped plasma-like oscillations (for relatively small initial population imbalances), or whether dissipation at early times is instead dominated by vortex- and sound-induced dissipation (for larger initial imbalances). The latter defines the effect of the thermal cloud on the condensate dynamics, with a reversal of roles, i.e. the condensate being driven by the oscillating thermal cloud, being observed when the thermal particles acquire enough energy to overcome the barrier. Our findings are within current experimental reach in ultracold superfluid junctions.