% Original data
s1 = ["A" "B" "C" "D" "E"];
s2 = ["A" "E" "1"];
% Create a buffer of empty strings to fill the gap
s0 = ["",""];
% Combine into one string array
s = [s1; [s2,s0]];
% Write to file
cellwrite('s.csv',s)
The best way to combine the string array will largely depend on how you need this to generalize. For example, if you have a long list of string arrays, you would need to loop through them to create the buffer.
