When I got my cotl and his dam, they were both pretty wild. We never could get the mare calmed down to halter/tie her away...what we did was put a panel in one corner of their pen (we had them in our round pen) and put bars over the top, low enough for baby to get under and eat/get some time away from mom. It was just a panel so they could see/touch each other, but momma couldnt get in and bug him or steal his food.
Keep us updated on your colt! Hope he's feeling better soon