Well, I was wrong. I had a hunch I was wrong, and so I finally got the chance this morning to revisit the chapel. Yes, the windows are lit from behind--they just were off when I visited the first time, and I couldn't find the switch.
In case you can't remember, the original Millcreek chapel had two windows--one facing outward that was added around 1910, and another facing inward that was added in the 1930s. They are virtually identical, but there are some differences.
Here is the original 1910 window, which is in the new building's south lobby:
And here is the 1930s window, in the north lobby:
There are distinct differences between the two, particularly in the colors of the glass. The older window has some coloring that is non-traditional for a stained glass setting of the good shepherd; whether this was intentional or not is unknown. Thank heavens these windows can still be enjoyed properly!