It should not be necessary to use entity managers directly. Everything should be possible via the HistoryService and then the HistoricVariableInstanceQuery or one of the other historic queries that are offered.
Ok understand your point now. You would like to update an historic variable.
You could use the ManagementService executeCommand method and create an inner class Command implementation that gives you an instance of the CommandContext. And then you can get the HistoricVariableInstanceEntityManager from the CommandContext.