Why shun Col. Autumn's plans? He is the one who refused to massacre everyone in the Wasteland. He gave James a chance to surrender, offered him a job, warned him several times that this is no joke. Of course if you support the Enclave's past plans of global genocide go ahead, but you suggesting cooperation with the BoS suggests that you don't like the idea of a mass graveyard.
But there is hope after all. The Enclave is not dead. Elder Lyons admits this himself (while not generally the most reliable person, I trust him in this obviously) and the Enclave most likely still possesses several bases and numbers enough to sustain population. There may be unopened vaults with people in them.
Whenever the next Fallout is announced, I will 24/7 campaign for Enclave involvement as the good guys, or at least as the equivalent of Mr. House as in the "neutral third guy".