The Homestead has quite a lot of things associated with it, so instead of deleting it as a whole, I would probably change the story element that allows the player to go to the Homestead at all. The simplest method would probably be to either change the Story element that teleports the player when they first encounter a Star/Blood Stone, or change the Star/Blood Stone templates such that they don't trigger the Story element.
If the Homestead is never reached, then the biggest change to the main campaign would be that the players no longer have access to the Teleport Pyramids (and of course losing access to the goodies that the Homestead contains). There would probably be an issue with the end game as well, but besides that there shouldn't be too much of an impact, since most of the game can be played without going to the Homestead at all.
