You back takes a little beating from running, due to the shock of your feet travelling up through your hips and spine. As you said though, sitting puts more stress on your lower back than running does itself.
Best thing to do is probably cut back on the distance you run and avoid uphill runs. Also you could try switching to something which has less impact on the body [cycling or swimming]. Keep deadlifting and you'll strengthen the muscles in your lower back which will help.
Take it easy a bit... Have a nice hot bath or something.

)
Also make sure your posture is good during your run - nice straight line between head, shoulders and hips.

Try to minimise the impact on the road too by not planting your heels on the floor when you run.
Hope that helps a little.
Russ.