Recently I had to remove a batch class from a system. This feature is going to be available through the UI in a soon to be released version of Ephesoft but for the mean time here is the SQL used to remove a batch class with an id of 3.
DELETE FROM batch_class_plugin_config WHERE batch_class_plugin_id IN (SELECT id from batch_class_plugin WHERE batch_class_module_id IN (SELECT id from batch_class_module WHERE batch_class_id = 3));
DELETE FROM om batch_class_plugin WHERE batch_class_module_id IN (SELECT id from batch_class_module WHERE batch_class_id = 3);
DELETE FROM batch_class_module WHERE batch_class_id = 3;
DELETE FROM batch_instance WHERE batch_class_id = 3;
DELETE FROM document_type WHERE batch_class_id = 3;
DELETE FROM batch_class WHERE id = 3;