First of all, generally, yes, it would, especially over several controlled matings, the ability to observe and assay embryos, in vitro fertilizations, etc.
Might the incompatibility be due to another organism, parasitic or otherwise, that the other frog population had not been exposed to affecting interpopulational fertility?
No. It's not fertility that's affected. It's a developmental problem in the offspring. Southern females and northern males have lots of babies - the babies don't (can't) develop into adults because of genetic deficiencies.
Consider also that their research is based on comparative molecular studies between the mitochondrial DNA of the northern frogs and the southern frogs. You mentioned Occam's razor. Is it more likely that an external force is causing such differences between them (especially developmental problems) or that the observable differential molecular sequence is causing a differential phenotype? :)
Here, extra legs and here Scientific American, page 2 mentions parasites other causes are noted.
It takes no great leap to find potential for attribution here, well outside of aberrantly rapid evolution. Isolated populations will be exposed to different environmental factors, including vegetation, chemicals (natural and manmade, the latter in precipitation or runoff) and quite possibly different pathogens. One population exposed to a chemical (natural or manmade) or a pathogen, be it viral, bacterial, fungal, or parasitic, will naturally successfully breed only those who can adapt to or are resistant to that pathogen or chemical and still produce viable young.
That change could handily occur in just a few generations, not even 8000 years.
The other population, not exposed, might not fare as well if the pathogen or traces of the chemical are transferred in the act of breeding and that population has little or no natural resistance to the pathogen.