Arlin Stoltzfus has a guest blog series on the conflict between Mutationism and the Modern Synthesis on Larry Moran's Sandwalk:
Introduction to "The Curious Disconnect"
The "Mutationism" Myth I. The Monk's Lost Code and the Great Confusion
Theory vs Theory
The Mutationism Myth, II. Revolution
The Mutationism Myth: III Foundations of Evolutionary Genetics
If I understand the basis of Stoltzfus' arguments correctly, he seems to be arguing that Darwin's original formulation of natural selection, which was later incoporated in the Modern Synthesis, implicitly depended on models of variation and heredity different for the models of variation and heredity that geneticists observed. Thus, evolution is more-or-less non-Darwinian in the strict sense that, to the extent that Darwin's original formulation depended on the his models of varaition and heredity, evolution does not follow Darwin's initial assumptions about variation and heredity.