Is anybody having flashbacks to the early 90s story "The Crossing" in which the original Tony Stark died and was replaced by the teenage version who was transformed by Franklin Richards into the Tony we have now?
Marvel's glossed over that a lot... But technically Teen Tony is the current Tony and the Tony who founded the Avengers died after being brainwashed by kang into becoming a traitor.
I hate to see such a story revisited on some level and yet I think you could PARTIALLY redeem Tony by swapping back to the traitor who worked for Kang.
I mean, sure, he took DNA samples from heroes with the idea of cloning them... But he wasn't the one who acted on it.
You could bring back the "original" Tony and have him horrified at what the "current" Tony did with the plans he set into motion. Thus, the emotional consequence of being a rat bastard would weigh on Tony Stark but you'd be free of the Secretary of Defense baggage as well as the baggage of being an outright fascist.
And along the way, you finally iron out the wrinkle that the Iron Man we have isn't technically the original Tony Stark.
Reed's a bit trickier to redeem but the words "Dark Raider", "Brute" and "Ovoid Mindmeld" all seem like the start of copouts I'd accept to get the FF back together.