It’s not just the atmosphere that’s an issue though, having a laser in earth’s orbit track something on mars’ surface and vice versa would require some incredible tracking, it would be easier to go from orbit to orbit

It's not that hard with modern electronics. Telescopes with adaptive optics have been doing that since the 90s. Also beware that a laser doesn't remain perfectly coherent over many kilometers (let alone millions). So it's not like you need to perfectly hit a satellite dish area of a few m^2 on the surface of mars from earth. It's not really any harder to do from the surface than from orbit. In fact it might actually be easier since you don't just have to account for the rotation and orbit of earth but also for the orbital velocity of the relay.