Except, he's the guy in charge when he removes President Eden from power. You never fight the genocidal faction, they're allied with you.
Colonel Autumn's rebellion against Eden is possibly the laziest cop out in Bethesda's recent history.
"Alright, so the story's a long ways so far, but it's looking pretty linear. The player has no choice but to help the Brotherhood no matter what. How do we fix this?"
"Oh, I know Mr. Howard. Maybe let the player help President Eden if they choose to?"
"That's good! What do we have to do to make it happen?"
"Well, we'd need a new end quest line that really shakes things up. An entire new set of scripted events and occurrences that puts the player on the Enclave's side. They'd need to help fight off waves of Brotherhood attackers on the Water Purifier, and as an added bonus, they could even have a boss fight with Liberty Prime. The Broken Steel DLC might begin with a Brotherhood agent forcibly activating the Purifier while the player's nearby, and the player seemingly dies while the Brotherhood come and steal the FEV sample Eden gave them, but the Enclave uses the same anti-rad drugs they used on Autumn to keep him alive and bring him back. Broken Steel would involve raiding Brotherhood outposts, taking GNR for the Enclave and overtaking its broadcast, allying with or killing the Outcasts for good, then launching a final assault on the Pentagon itself, Vertibirds flying all around, Brotherhood and Enclave soldiers in desperate struggle, and the player, of course, having to destroy Liberty Prime, maybe by taking a Vertibird to the Mobile Platform which has been overtaken by Brotherhood troops, fighting through them and setting the cannon there's target on Prime himself. It would end with with the player regaining the FEV sample and being left with a decision, as Colonel Autumn urges them not to follow through with Eden's plan and to instead join his own splintering faction of the Enclave, while Eden insists his plan will truly revive the wasteland and let life there begin again. This is the moral choice on the player's part - Eden or Autumn? Either way they congratulate you as a patriot. If you side with Autumn, Enclave troops utilize his self-destruct and Autumn becomes the new acting leader of the United States Government. If you side with Eden you get a mini quest where you track down Autumn and his loyalists and kill them. A fitting end and plenty of player choice agency given!"
"Nice, nice, how much work and planning would that take to implement?"
"A lot."
"Dammit Mark, we're Bethesda developers, you know we can't do anything that requires work or thought! Scrap the whole thing! Just have the player fight the Enclave and help the Brotherhood no matter what they do."