Just speak with the BoS chief McNamara (or something, i forgot) and tell him NCR's plan. If you removed him from his post then you'll have no option but to destroy them.BTW, when NCR asks to destroy brotherhood what can I do to save brotherhood - I mean can I speak with any NCR higher authrity so that they can alter Moore's command
and don't forget to save the trapped Ranger inside Vault 3.