There are two canon universes now.
The comic universe of the comics, novels, and telltale games.
And the tv show universe of the show, webisodes, and survival instinct.
They are never going to be together. They are both drastically different and will not work as one medium for pretty obvious reasons.
As for the Gov. we see his fall instead of him just being crazy the whole time. (for the comics we do see it in the novel now but I doubt we do in the show.) It's pretty much established tv gov was Philip the whole time. Milton knew him before all of this and he is actually in the picture with his wife.