Discrete Baker's Map
Pyth, 25 19 18 bytes

msC_dcs_Cmck/lk2Q2


Online demonstration. It uses an 2D-array of chars. 

Array of strings is one char longer (19 bytes). Online demonstration

Explanation:

         m      Q    map each string k in input:
            /lk2        calculate half the line-length: len(k)/2
          ck/lk2        chop k into pieces of length len(k)/2
                        results in two pieces
        C            zip the resulting list
                     results in a tuple ([first half of strings], [second half of strings])
       _             invert the order ([second half of strings], [first half of strings])
      s              sum (combine the two lists to a big one
     c           2   chop them into tuples
m                          for each tuple of strings: 
 sC_d                        invert, zip, and sum


The last part is a bit confusing at first. Let's assume we have the tuple ['DEF', 'JKL'] (I use the example from the OP). 

    d  (('D', 'E', 'F'), ('J', 'K', 'L'))   just the pair of strings
   _d  (('J', 'K', 'L'), ('D', 'E', 'F'))   invert the order
  C_d  [('J', 'D'), ('K', 'E'), ('L', 'F')] zipped
 sC_d  ('J', 'D', 'K', 'E', 'L', 'F')       sum (combine tuples)