I don't think you'd have to wash the yarn it was attached to. I would take a piece of contrasting yarn (make sure it's colorfast! I'd use a synthetic yarn), thread your stitches onto that and knot it really well, cut your working yarn, then carefully handwash it with some woolite, or even a small amount of mild laundry detergent. Since the markers are washable, they may very well come out.
If you do this-a tip for getting your stitches back on the needle afterward--use a needle size two sizes smaller and then slip your stitches from that back onto the needle you will knit with.
If you can't get the stain out, you might go on Ravelry and see if anyone has any of the color you need to sell or trade.