I had this happen to me shortly after I started quilting, my husband brought home TWO quilt tops that his mother made, back in the day of cereal box templates and scissors.
Trip Around The World with several borders half sewn on with intent of being mitered. :-(
These things were huge! Being new to quilting I decided to use a flat sheet to back them, had to remove a border to fit a king sheet which was no easy task as she used a very small stitch length. Needless to say my wonderful husband was in the dog house for a time.
Moral to this story is that after I fixed the borders, quilted and bound them, I gave them to her on Mother's Day and her joy at having them finished was well worth my time.
Don't stress too much, your MIL will be so happy to have her top made into a quilt she wont notice the imperfections that you as A QUILTER will (we tend to be perfectionests) and because she's family you will earn alot of DIL points :-)
Good Luck!