So sorry about the blue marks in your beautiful quilt. I having nothing to offer except I had the same thing happen (and it was a quilt for a friend too) w/one of those pens and I did not iron my fabric. It just stays in some fabrics better than others. I promptly threw away all the pens like that I had. Honestly it is scary marking quilts because you think something is safe only to find out after the fact that it was not. I fear I will have issues w/the quilt I am hand quilting right now because I have used chalk that I thought would be safe and it turns out it may not be either. I will from now on test on all fabrics that will be used in a quilt before marking.
I hope you find a solution to your problem, and even w/the marks I know your friend will love it, mine did.