I think the issues with polyester thread on cotton fabric have more to do with piecing than with the actual quilting. Particularly if there is less than a 1/4" seam. Jan from Be*Mused wrote a post about a quilt that she made in the 80s for her sister. I'll link the article but in essence she shows where the cotton wore away from the poly core and cut through the seam of the patchwork. I think many factors could be at play here but, in my opinion, this is the type of situation most people think of when the question of piecing with polyester thread comes up.
http://bemused.typepad.com/bemused/2...r_caution.html
I think that most people would agree that with the strength of the three layers (and more when quilting over seams) and the improvement in quality of polyester thread there is no danger when quilting with polyester thread.