The Mystical versus the Spiritual
The characters in the story are earthly humans, and most are devout, or at least believers of some kind. However, representative of general belief at the time, there is also an element of paganism in the story, and other characters, such as Merlin, and the fay who impregnates the Duchess of Austria, are mystical, pagan figures. There is a distinct message in the story that implies there is a battle between the "good" forces of Christianity and the darker forces of Paganism. When Gowther pleads with the Pope for absolution and effectively gives his life to God and humility, he is saved. The text shows the constant battle between the two and also suggests that Christianity can emerge victorious.
Absolution
The Pope absolves Gowther of his sins but he also gives him a considerable penance as well; he does not simply verbally absolve the sins and allow Gowther to move on. Gowther also participates in his own absolution in that he becomes a better and more godly person. He starts to understand gratitude, and he summons his courage to fight alongside the Emperor in defense of his kingdom. He is constantly aware of his own past deed and continues to refer back to them, for example building a new abbey next to a convent so that the nuns whom he burned alive can be remembered and a prayer said for their souls every day.
Political Situation of the Time
Because the ruler posing a threat to the Emperor is the Sultan, the text brings into the story the political feeling of the day and the threat that was posed to the civilized Roman Christian Empire by the Moors and the Arabs, in this case, in the form of a Sultan who wants the Emperor's daughter as his wife and also wants the lands he presides over as well.
The forces of the Emperor are courageous and gallant knights, whereas the text describes the Sultan's forces as "screaming hordes" and makes it plain that they are a rabble rather than an army. This is another way of emphasizing the way in which the Arabs were seen at the time of the text's writing.