All analogies are faulty -- they're analogies, for crying out loud. At some point, Deflategate will have to be dealt with on its own terms. Until then, these analogies aren't terribly useful.
Everyone knew Gaylord Perry was a spitter, but it wasn't commonly assumed that Brady deflated balls throughout his career. (Until now, that is.)
Corked bat? That's closer to the mark, because Sammy Sosa wasn't assumed to have cheated until the awful moment when he was "exposed." And his legacy has taken a huge hit.
It remains to be seen if Brady's transgressions will result in the denial of post-career honors, HOF, etc. However, we know how the court of public opinion has dealt with MLB juicers. It's like they never existed. All those haters who wished Brady would "go away" just might get their wish.