I would say that the moral of this story is that taking an empire and trying to rule it (as the British did in India and elsewhere) is nearly impossible to do well and is harmful to the people who take the empire.
In this story, the British characters, and especially Fleete, are completely ignorant of the empire they are supposed to rule. Because of this, Fleete does something really stupid without necessarily understanding that it was. It is hard to run an empire when you don't/can't understand the ways of the people you're trying to rule.
It is also clear from the story that power has corrupted the Englishmen. Because they are the colonizers, they feel that they are so superior that they can do whatever they want.
In the story, ignorance and arrogance lead to terrible consequences. Kipling seems to be saying that this will be the case in real life as well.
Let me also fill you in about the original context of the mark of the beast. It comes from the last book of the New Testament and the mark of the beast is 666. There are a lot of theories about this number, but it is probably best to interpret it in two ways.
1. Like the previous post, the mark of the beast is probably referring to an empire, or better yet, the memebers of that empire.
2. The mark of the beast should also be seen in contrast to the number of God in the book of revelation - 777. I think what the book of revelation is trying to say is that the number of the beast will always fall short of the number of God. In the end, God's kingdom will win.