división de cadenas mysql

Puede hacer esto usando un procedimiento almacenado

DELIMITER $$

CREATE FUNCTION strSplit(x VARCHAR(65000), delim VARCHAR(12), pos INTEGER) 
RETURNS VARCHAR(65000)
BEGIN
  DECLARE output VARCHAR(65000);
  SET output = REPLACE(SUBSTRING(SUBSTRING_INDEX(x, delim, pos)
                 , LENGTH(SUBSTRING_INDEX(x, delim, pos - 1)) + 1)
                 , delim
                 , '');
  IF output = '' THEN SET output = null; END IF;
  RETURN output;
END $$


CREATE PROCEDURE BadTableToGoodTable()
BEGIN
  DECLARE i INTEGER;

  SET i = 1;
  REPEAT
    INSERT INTO GoodTable (col1, col2)
      SELECT col1, strSplit(col2, ',', i) FROM BadTable
      WHERE strSplit(col2, ',', i) IS NOT NULL;
    SET i = i + 1;
    UNTIL ROW_COUNT() = 0
  END REPEAT;
END $$

DELIMITER ;