Do not store them in two separate variables, but use a cell or struct array! It is the contents of variable that should vary, not the name ...
img{1} = imread( i1 );
img{2} = imread( i2 );
%drawing it on the back buffer
X = randperm(2) % [1 2] in random order
myTexture = Screen( 'MakeTexture', window, img{X(1)} );
Screen( 'DrawTexture', window, myTexture, [], rectL );
myTexture2 = Screen( 'MakeTexture', window, img{X(2)} );
Screen( 'DrawTexture', window, myTexture2, [], rectR );
