I solved this problem by using the fairly recent (~18 kya) expansion of marine populations onto the Sunda Shelf in South-East Asia as a calibration point, rather than the traditional divergences. These expansions came with rising sea-levels following the last glacial maximum (see figure below). I used a two-epoch coalescent model implemented in BEAST to get mutational depths. Results for three invertebrate taxa strongly suggest that their rates of change are elevated above traditional molecular clock calibrations, within the timescale from 0-3 million years ago, thereby lending support to the time-dependency hypothesis.
I hope that the method, carefully applied to well-documented expansions, can be helpful in providing more accurate (and taxon-specific) assessments of the molecular clock at phylogeographic timescales, with appropriate confidence intervals. The method was recently expanded upon by Thierry Hoareau!.
Crandall ED, Sbrocco EJ, DeBoer TS, Barber PH, Carpenter KE. 2012. Expansion Dating: Calibrating Molecular Clocks in Marine Species from Expansions onto the Sunda Shelf Following the Last Glacial Maximum. Mol Biol Evol 29:707–719. doi:10.1093/molbev/msr227
Here is a link to a tutorial for how to set up your own two-epoch model in BEAST.