Good luck. How frustrating.
I used to put pins in the cut end of fabric that I used a few strips of every once in a while. This happens often with white, black or other neutrals that go with anything, of which I usually purchase yards and yards at one time. Now I set the machine stitch to "very long" and sew a few (just 2 or 3)stitches about 3 inches or more from the cut end. Lift the presser foot and pull the fabric ahead and make a few more stitches, and do that one more time. Be sure the fabric is flat between stitching. Then, when I want a few more pieces off that fabric, the end is still perfect. Saves a lot of time getting the end "cuttable" and saves fabric because you don't have to keep trimming the end each time. When it's time to take out the stitching, just pull those loose threads between the stitches. No pins to rust.
I don't know if you can get it or not anymore because I have had mine for several years but the product I use is called "Penwalt Erusticator". It states on the bottle that it removes rust from cotton to silk. I believe I purchased it at a hardware store. It works really well on fabric..just takes alittle bit and the rust comes right out...If you can't find this particular product I'm sure there are others out there that do the same thing...Good Luck...
What about Retro Clean?
I was in a quilt class with Pam Clarke last year and showed her an antique quilt top that had the safety pins left in for who knows how long..She told me to quilt the quilt and finish it and then soak it in the washing machine using Oxi Clean and that should get rid of the rust..I haven't done it yet..but she's the expert. =)
I don't have a clue but I have found several of these answers to be very beneficial!
I have used Whink to remove rust stains from clothing and it works great. Just be sure to follow the directions on the bottle.........