HI Sactownchicks, well, you need to be able to clean it.
If your gravel was several inches deep over a layer of dirt or sand, you could probably just pick up any major poop with a shovel or rake and hose the rest down. Adding deodorizer or neutralizer of some sort if needed, not sure the right thing here, maybe garden lime?
I'd say the EASIEST solution is to take the time now to get it clean once, whatever it takes.
Then scatter some straw, a thin sparse single layer, in the run from then on, not a lot, just enough so that the poop can stick to the straw. Then you can rake it out once a week or more if needed & replace. You might even get away with leaving it until a rain or something. If the rain is planned, you might even think ahead and rake it out, leave it gravel and let the rain wash the rocks for you.
You might think about a new design for the future.
We had a couple of coops like that and we scattered Quickcrete over our clean 2" bed of decomposed granite and watered it in, making a rough concrete floor. Then use the scattered straw method. Works so much better for us on those runs now.
Best of luck to you!