I don't think he realized how bad it was until they rigged the election. I think he now understands just how corrupt the Washington DC cartel is.
While I think that Milley is a douche, there have been generals undermining the presidents they served under from McClellan to MacArthur. All sorts of people think they know better than their boss does. It’s hardly a sign of a secret cabal or any kind of vindication of your views on the cause of the Civil War.