During construction, there will be a skinny path to walk to ET's front entrance along the work walls on your left.
I think Spongebob Storepants and ET's entrances will remain the same, and a path will be left to access them, along with the restrooms in between them. That path will also be used for Nintendo exits as well...
Like Diagon Alley has two exits, one near the brick wall entrance and one further down that spits you out elsewhere in London, Nintendo will have exits that spit you out in front of Spongebob and ET.
If anything, this might actually make ET more popular, if people are being funneled into it after leaving the new land.
There's of course still been talk of re-routing the ET entrance to the other side, but this would've been a lot easier before they created the NBC Media Center out of the Allah Gardens. As of now, as far as I know, they're just gonna leave a path to ET next to Nintendo. Probably with a new big sign on the the main path so people know what's down there.