yeah, I think you need to go beyond BABIP. Perhaps, neither is an anomaly and they are two very different samples. For example, Major League hitters are a lot better than minor league hitters, so maybe they are better able to take advantage of the new rules. I don't know how that would work, but I don't know if what happens in the minors would be expected to translate to the majors.
If I remember correctly, there was also not a big difference in stolen bases with the changes in the minors, but there has been a substantial difference in the majors.