Well, the facial muscles are innervated by cranial nerves, which do not run through the spinal column (the L in ALS stands for 'lateral' referring to the disintigration of the lateral portion of spinal cord), and the eye muscles in particular send input to several motor nuclei . Since the progression of ALS tends to start in the upper or lower extremities and progresses proximally, I would guess axon length might be a factor in cell survival. Also, since ALS affects both upper and lower motor neurons, I would guess the eye's redundancy of having several motor nuclei might preserve its motor capacities.