I use a black frixion pen to mark my quilting on all my quilts. I have never had a problem. Once I used a lime colored one and when I ironed the marks off it did leave a ghost line, but it was so faint that it didn't ruin the quilt for me. I figured most people would never notice it, and no one ever did. However, I only use black ones now, and I have used them on both 100% cotton and cotton/polyester blend fabrics without problems.
The one thing I did use that did ruin a table runner for me was yellow chalk, so I would recommend never using it.