Before digging up the rocks or pouring cement you might want to check and see if the rocks are there because of a water problem. If you cover the rocks the water may start to come in the house. I think the reason for the rocks may have been done for drainage.
That said you have done a beautiful job. The overgrown area probably why the snakes were there I bet after a few more months they will move on and find a more habitable place to live because they no longer have the undisturbed over grown environment as before. That area in the condition before you fixed it up was perfect. They had plenty of food.....mice, and plenty of bugs.
Try lighting citronella candles and line them up they do not like to hang around fire.
