On the one hand, no normal dirt (that you could use for a veg garden, say, as opposed to fill that should be in a toxic waste site) is going to harm your chickens.
On the other hand, putting a deeper layer of dirt in your coop is IN NO WAY going to protect them from things that dig. And will require significant engineering of the boards that would retain it.
You'd be better off making a broad wire-mesh apron (use 1x1 or 2x4 galvanized wire mesh, in a heavy gauge) that lays on the ground all around the coop and is pinned well to the ground or tucked under a layer of turf or rocks or whatever. And of course attached to the base of your coop wall as well. A 3-4' apron, well secured, will prevent anything except rats from tunneling in (and nothing short of concrete is really going to keep rats out anyhow). It is relatively easy to do, and can simply be bent to fit over the existing tree roots and irregularities int he ground.
Good luck, have fun,
Pat