In this shot Father Flynn is looking at this stained glass window while he walks, and pauses to consider it, wearing a face of dismay if not guilt and regret. The eye can be presumed to be the watchful eye of god that is all-seeing. The eye seems to watch Father as he walks and his expression seems to be under the weight of the stare. The sight of the window seems to inspire introspection in Father Flynn, suggesting that he is perhaps considering his standing in the all-knowing view of god. This is supported by the fact that the window is the only source of light in the shot; the light of god illuminates all and "brings to light" any secrets father might have. The radiating design around the eye further signifies that the light originates with god. An interesting comparison can be made between the light of this window and Sister Aloysius' light bulb, which keeps going out. Perhaps the connection can be made here that god's light never goes out while Sister's light is ephemeral and untrustworthy, incubating better the seeds of doubt in her mind.
Furthermore the wood columns on the banister stretch from the top of the frame to the bottom, and fill the frame horizontally as well. The columns seem to represent the bars of a jail cell, which is emphasized by the fact that there is no way around the bars in this frame, we can't see over them or where they begin or end. This "prison-cell" symbolism could illustrate that father is guilty, and feels trapped by his guilt under the condemning eye of god; which could be supported if Father's look in the following shot is interpreted as one of guilt. The prison-cell metaphor could also symbolize Father's disconnection from god; if he is evil and has "stepped away from god" as sister Aloysius suggests, then he has lost touch with god, which is supported by his sermon about feeling lost and in doubt at the beginning of the film. The shot could also be interpreted as father feeling the same way but about something he has done at a past parish, rather than abuse.
On page 42 of Molly Sweeney, Molly describes her first experiences of vision after her operation; "Every color dazzled. Every light blazed. Every shape an apparition... And all that movement -- nothing ever still -- everything in motion all the time..." With her expanded sense of the world Molly seems to have regained, in some ways, some of the wonder of childhood that can be experienced only through massive raw sensory input. Because her new sight can only be compared to her previous understanding of pure darkness, every light and color is extremely significant, like the first strokes of color on a blank canvas. Being a child again has it's drawbacks, however; all of the new information can become overwhelming and frightening. At times her visions appeared "aggressive, dangerous. So that after a time the mind could absorb no more sensation... and the only way to escape -- the only way to live -- was to sit absolutely still; and shut the eyes tight; and immerse yourself in darkness; and wait... slowly open the eyes again. And emerge. And try to find the courage to face it all once more." This passage brought to mind an experiment I read about recently in which baby monkeys were given surrogate mothers after birth that simulated their real mothers. (The experiment: http://darkwing.uoregon.edu/~adoption/studies/HarlowMLE.htm) When a random element was placed in the enclosure, such as a noise-making toy, the baby monkeys would become frightened and cling to their fake mothers; they would stay there until the fear passed and they they would leave the mother to inspect the new thing in the cage. This dependence on a familiar comfort reminds me of Molly closing her eyes to escape the lights when they became too frightening. For the first few months of life, mothers are essentially all that babies know; they are a child's base of comfort and security in an unfamiliar world. For Molly, the world being dark is her security; when it is dark there are nothing to be afraid of.