The stained glass was created as a plot device to help tell the story of Easter without having to show Jesus as a vegetable.
The oval picture on the wall in the Gilberts' home is Charles Dickens, author of A Christmas Carol which this video is based on.
Although this film was produced and released after VeggieTales: The Star of Christmas (2002), that story was actually written later, as a sort of prequel. The two were written as a matched set of "bookends" for the two most important holidays in Christianity.
The stained glass artwork during "Hope Song" is animated (some scenes more than others). The final panel, showing Jesus resurrected, has a very subtle animation of His ascension.