I didn't reply to the previous post, but did think about it ;-) . My opinion is that there were 3 'classes' of quilting issues: (1) a piecing error where a block was obviously turned the wrong way 'round and (2) excess fabric issues, either puffy blocks, puffy center, or wavy borders and (3) Backing or Batting provided was too small.
If it's a piecing error, I would say that 100% of the time the long armer should stop and call.
The too much fabric issue is a grey area. I worked with a professional quilter who would routinely fix these as part of her quilting service and never call the customer. As far as they knew, she just quilted it out. The down side of this is some customers continue bad habits (especially the wavy borders).
Issue three would probably also be a stop and call. I wouldn't trim the top to fit the backing in case the quilter was aiming for a specific measurement. If there were enough backing where you could cut a strip from the length and add it to the width (or vice versa) I would suggest this, but mention that there would be an additional charge. Most long armers charge extra for seaming a backing.
The kindness you did by fixing the top went above and beyond your job description, and it sounds like you didn't alter the size of the finished quilt, just squared it. I would just explain the problem to her. My guess is that she will probably be OK with it.