No, because there wasn’t really a plot for them to change. They don’t plot way far ahead in this show; there isn’t some unifying long-term storyline like in the first five seasons of Supernatural.
Aside from ‘how Sherlock did it,’ they plotted and scripted most of this season just last year. And now, Gatiss and Moffat mentioned they plotted out most of seasons 4 and 5 recently on a train trip. So they more or less write on a season by season basis. If they want to keep Mary, they just decide they’ll keep Mary. They don’t have to change anything.
