Well, we were told that "the universe has a way of righting itself" in season 3. I'm not sure if the impact will be too great. And Penny seemed pretty angry at Desmond in the past, so I can't really see them getting back together in 1996.
Look at it this way: she was shocked to hear from him in 2004 when he called from the boat; that was after the point at which Desmond changed the future - a different 8 years had passed between 1996 and 2004 from the 8 years we were previously shown. But Desmond was still on the boat, still in the Pacific and Penny was still surprised to hear from him. If history was going to change, it would have changed by then. But it didn't.
Look at it this way: she was shocked to hear from him in 2004 when he called from the boat; that was after the point at which Desmond changed the future - a different 8 years had passed between 1996 and 2004 from the 8 years we were previously shown. But Desmond was still on the boat, still in the Pacific and Penny was still surprised to hear from him. If history was going to change, it would have changed by then. But it didn't.
