I would say that external evaluations of articles could also be done by email through reciprocal correspondences between the journal manager (or editor in chief) and external reviewers, so the simplest journal workflow could be as simple as illustrated in the figure below:
As such, I think that some tweaks/modifications to Omeka code/structure, or at least building a theme or plugin that provide the framework functions illustrated in the picture above, would make Omeka as a good and clean journal management system.
By the way, the citation format already provided in Omeka is a good one, so it could be kept in any potential new theme or plugin to make Omeka as a journal management system.