Yeah.. unfortunately it was never really a vacuum, as PhD's had already infiltrated the CP labs and were a simple fit into this role. As with other CP labs there are advantages to having an MD director, but as it's not "required" and PhD's generally earn less salary and have a greater chance of being involved in grant funded research, a non-medically trained administrator probably sees this as a no-brainer. Clinical pathologists kinda shot themselves off the ivory tower many years ago with self referrals and various apparently questionable practices (similar to what we're seeing now in AP, although more a result of urologists, GI's, etc. running their own path), and billing I guess now works differently -- bottom line being it's less profitable to be a CP, unless perhaps you're running a large lab and paying some PhD's to do the dirty work.
There's a lot of rumbling about molecular being the growing big thing, but the same could be said of immunohistochemistry not all that long ago, which has already rolled into regular practice. I have a feeling it's likely to be just another "lab test" with testing modalities managed by the lab but interpretation primarily by those familiar with a given specialty, some in path and some not (soft tissue, heme, oncology, microbiology/infectious diseases, etc.), as already seems to be the case. Until someone puts forth some extremely compelling reasons for individual clinical lab departments to all be individually directed by an MD pathologist, not just medical director oversight by any ol' MD who need not know what a lab even is, I doubt this is going to significantly change. But, who knows.