We analyze, through molecular dynamics simulations, the temperature dependence of the thermal conductivity (k) of chain-oriented amorphous polyethylene (PE). We find that at increasing levels of orientation, the temperature corresponding to a peak k progressively decreases. Un-oriented PE exhibits the peak k at 350K, while aligned PE under an applied strain of 400% shows a maximum at 100K. This transition of peak k to lower temperatures with increasing alignment is explained in terms of a crossover from disorder to anharmonicity dominated phonon transport in aligned polymers. Evidence for this crossover is achieved by manipulating the disorder in the polymer structure and studying the resulting change in temperature corresponding to peak k. Disorder is modified through a change in the dihedral parameters of the potential function, allowing a change in the relative fraction of trans and gauche transformations. The results shed light on the underlying thermal transport processes in aligned polymers and hold importance for low temperature applications of polymer materials in thermal management technologies.