You can do whatever you want with any material. I used jeans on one side and cotton on the other side and no batting. I don't see the difference with your scrubs other than it will be a light kinda quilt. If you feel you need batting then cut a couple blocks from the scrubs and put flannel on the other side. So you would have flannel on one side , scrubs on one side and scrubs as the batting. It can work and most of the rag quilts I seen sew an x on them. But then again you could sew lines or whatever you want to keep it all together.