I did have a 'problem quilt' years ago. I rented a long arm and for whatever reason the last 3-4" of the darn thing would not quilt right. I removed the thread twice! No dice. I thought poo, poo, poo! Finally I just said forget it. Clearly that area was not meant to be quilted. Although it still bothers me, that strip is still not quilted.
If your materials are of good quality, it should be alright to remove the stitching. Just get comfy and have a new, sharp ripper.