I was dissappointed with how the BoS is handled as well. I had them side with the Republic and if you blinked you completely miss them in the final battle. It would have been cool to give them Helios One and lay waste to Caesar but no such luck. Or if it is I did not do the various quests in the exact order required to enable such an ending.
I found they were quite useful in the final battle, personally. There isn't a way to give them HELIOS, you really only get the two options if you're siding with the NCR - you either destroy them, or if McNamara is the elder, you can get your treaty on.
Seriously? The game guide says I could align both NCR and BOS, that being my plan. So my only option is to destroy the group I just became a part of. Stupid. The quest doesn't tell me to how to destroy or align the BOS. It just puts the marker directly in the middle of the sand in between all 3 entrances to the bunker. Makes no sense.
You can. If Hardin is elder, however, as stated above, you must destroy the Brotherhood in order to side with the NCR. Them's the breaks; Hardin's not much for making peace.
On the whole, this is not a bug.