I guess my only question would be how much do the scrubs fabrics fray? If they are cotton or blends I don't see why they wouldn't work. I've made several rag quilts for charity and do not put batting in them, just use a third layer of flannel in between. And I too have seen them made with cotton and flannel or even just cotton fabrics with batting between. Maybe you could sew up a sample quilt of just 8 or so squares, clip it and wash it and see what happens.