Much of the theory is based on the fact that we don't get much of a physical description of the Diurnal. Thank you, Wilshire. I have long been a lurker in the forum but finally the lack of people around me to discuss this amazing series with got the best of me and I joined. 
One issue with this, or course, is that the Diurnal is "a fan of mirrors that reflected the Sun" and might well be a Gnostic artifact, made by Emilidis. The way the bomb is desribed is nothing like that though, "It was no larger than a dollhouse, but seemed larger for the piping that enclosed it—a scaffold that somehow held the interior cube without touching it." In other words, it would seem to be a tesseract. I like the theory, but I don't think the text bears it out.
However, to take this another direction, I do believe that Kellhus knew that the bomb was there, what it was, and what it would do through the Visions and the Voice he hears. The question of why the bomb was down the well seemed obvious to me at the time of reading it, that they wanted to blow the top off The Well and have everyone fall down it, just as they did to Titirga. Kellhus anticipated this and that is why he was, from the moment they got to Dagliash, excavating the Well. Aurang realizes this and so pops in to set it off early, which again, is antcipated by Kellhus. This could explain why he says it is "a good thing" since it validates his visions as true, proves that TTT is intact and is proceeding, that all the sacrifices are not in vain.