The use of Latin signifies not only a superior education and the class that goes with that (western values vs. values of the orient, which was how Burma was referred to), but also connotes religious values in that the traditional western Church, developing out of Rome, used (and sometimes still does use) Latin in its liturgy. In saecula secularum concludes various prayers, including the Lord's Prayer, and means in that context "forever and ever," and is geneally followed with a conclusive and affirmative "amen." (The literal translation, according to a Latin teacher I know, is "for centuries of all centuries"). Orwell uses the phrase and similar phrases ironically, to call attention to the very lack of holy motives behind England's imperialist agenda. One aspect of that agenda was to "convert the natives" to civilization and the religion that goes with that, which, as he shows in the story, might not be as righteous in its values as it pretends to be. Just as religion uses a form of terror (the fear of hell) to encourage people to "be good," so the colonialist regime imposes a reign of terror (in terrorem) to ensure people submit to the rules it imposes.
Orwell uses a few words and phrases in the story which he leaves untranslated and in Latin. There are English equivalents to these words and phrases, but Orwell leaves them untranslated to show that the narrator who tells the story has been educated in European schools. Latin is a required course for schools in Europe so it shows the reader the education that allows the narrator to reason philosophically. His use of Latin delineates the class system that is in place in Burma due to the European imperialists that are tyrannizing the region. He also grasps more fully the weight of his actions possibly more than the natives do about shooting the elephant. The natives concern is with getting the elephant shot so they can strip it and use it, they have no moral dilemma facing them about shooting an animal.
He uses the Latin phrases in saecula saeculorum and in terrorem. ". . . as something clamped down, in saecula saeculorum, upon the will of prostrate peoples". This means "forever and ever" and he uses it in reference to the "unbreakable tyranny" that reigns over the region. "But I thought the noise might be useful in terrorem." Which means a warning or deterring others through the use of fear.