If you already have the locations of the eyes, then it's easy :) Here's an outline:
%// left eye - right eye
pos = [ 30 90 %// X
80 40]; %// Y
%// The angle equals the arctangent of dy/dx
angle = atan2(diff(pos(2,:)), diff(pos(1,:)));
%// Rotate in the opposite direction
img = imrotate(img, -angle);