I have an idea you might consider...since taking out the stitches might be a problem why don't you embellish the design? Perhaps you can get some sew on or glue on sequins in the shape of stars or snowflakes. You could then put them on the design radomly but making sure you hit the real puckered areas. I think they would make the eye see the overall design rather than seeing areas that might be less than perfect. I actually thing the whole design could become very cool !!
In any event, good luck !