After the first one, I would have explained that, while the quilting was good, it was NOT what I asked for and told her I would never use her for quilting one of my quilts again.
"The classes" told her that it was ok to DIRECTLY disobey her customers? She went to the wrong classes, or conveniently heard what she wanted to hear to justify what she does.
You change thread ONCE when you're long arming a quilt with the same color throughout. Sooner or later you have to change your thread anyway, so what's the big deal? If you're in business and getting paid for what you do, you really need to do what the customer wants not what's easier for you.
At the very least she should have told you what she planned up front and let you decide whether to leave the quilts with her or not. How hard is that?