I came into contact with the Brotherhood, helped them with almost everything, brought forth the new Elder, gained there trust. Now they want me to kill the Van Graffs which I
also have lots of friendly ties with, because they are helping the NCR with weapon supplies. Meanwhile, the NCR who are my preferred faction and friends wants the Brotherhood of Steel destroyed and neither side wants to resolve this peacefully, despite my 90 Speech skill. So I kill people I really like, kill people I really like, or work toward an ending I dislike.
I like to 'game honorably' and none of these choices work. If I DO destroy the bunker, is there a way to evacuate the BoS so they don't die? And so i'm not being bothered by approximately 50 guards with T-51B armor vs. 1 lone Courier in Recon armor, where can I find a stealth boy? Unless I rush in with Enclave armor, which I will be receiving soon, no way in hell i'll survive that fight, probably even with Enclave armor.