The Sequel gem qualified query column name with table double underscores
The answer is to actually qualify the column name using:
Sequel.qualify(:table, :column)
Or the equivalent shorter syntax:
Sequel[:table][:column]
resulting in:
employees = DB[:prm_master__employee.identifier]
.join(:prm_master__employee_custom_fields.identifier, :employee => :employee)
.where("termination_date >= ?","06/01/2012")
.or("termination_date = NULL")
.and(Sequel.qualify(:prm_master__employee_custom_fields.identifier, :employee) => "holderl")