I don't get what OPs relationship problem is about. If you care about each other, there should be no problem spending some time away from one another to pursue a hobbie you enjoy. You probably don't run much more than 1hr per day, so what exactly is this destroying in a potential relationship?
Stop being so prentious and sleep a few more hours with them if they want morning cuddles. Working late in the evening is hard on a person. Let them rest on the weekend and join them. Try relaxing on the weekend with them. Not every day needs to be balls out productive. The roads arent going anywhere. If you push your run to 9 or 10am, who cares. Even elites aren't that anal about running right on a specific hour.