Did a little research on my own, and here are the conclusions I was able to draw from the information I found:
BoB was a very large, very powerful alliance in EVE. They were also once very powerful. However, starting maybe two years ago, they went into a kind of decline. They were once very good in PvP, but, either due to stagnation in their organization or noobs who joined for the reputation, they started going down hill. BoB started losing. They could hold their own ground (mostly due the Sov advantages and their truely massive fleet of Titans), but they just couldn't win on the offensive. They lost several Titans, and numerous capitol ships. At this point, some of their higher ranking members began to get disgusted with the organization and with the other higher-ups who were getting full of themselves.
At one point, a BoB director used a secondary account to get recruited into the Goons. From what I understand, his initial intention was to become a spy. However, he grew to like the Goons, and their attitude towards the game. Specifically, it seems that the Goons are much friendlier to their new recruits than BoB is. The would-be spy then revealed his position as a director to the Goons and offered to use his position to help them.
The rest, as they say, is history.
So what does all this mean? Well, BoB had it coming. They were going to fall eventually (especially if they gave that much to one guy). Empires can only go up so far before they come crashing down again. It also might teach the organization a much needed lesson in humility (some of those guys are sickeningly arrogant). Still, it's a sad way to go. Had to happen eventually, though. In the long run, Goonswarm may have done BoB a favor, because the un-dedicated members probably won't stick around, allowing the good core elements to emerge once more.