The eyes are the window to the soul- I think you took a very literal meaning of that phrase. Doesn't it mean that the eyes are very expressive revealing your innermost thoughts... it's kind of like 'his smile didn't quite touch his eyes', or 'her eyes betray her mind'... I've read enough trashy romances to know this ;P

Anyway nitpicking aside, in a religious context, the spirit is seen separate from the body. In Abrahamic and eastern religions, the body is depicted as weak, prone to age and disease, something that causes the soul to suffer. In Abrahamic religions death is the only escape where depending if you have been naughty or nice your soul is whisked away to someplace in heaven or hell or some place in between. While in Eastern religions, the concept of rebirth is predominant. The soul is seen as something which is trapped in the cycle of death and rebirth (samsara). Bodies are again seen as vessels prone to disease and age, that causes physical and emotional suffering. Only by reaching spiritual enlightenment (moksha or nirvana) can one break free of samsara. How one does this differs across Eastern religions.