Joss never denied that the Alliance was meant to be antagonistic; he merely denied that they were meant to be 'the evil empire' (to use the words spoken directly by the Operative in Serenity); there are many things that the Alliance did that were abhorrent, but they were not done with deliberate malicious or evil intent.
If you need further proof that the Alliance, although antagonistic and misguided, was not an inherently evil organization, compare it to Wolfram and Hart, and I guarantee that you'll see the difference between truly evil actions (those of W&H) and the actions of the Alliance.