It's never fully explained why the Stanley 9000 computer would want Dilton, Veronica and Betty all dead, but not Archie, Jughead nor Pop Tate himself. Archie and Pop Tate interacted with the computer much more than either Betty or Veronica did.
The Stanley 9000 computer can --hear anything what's going on in the diner. But it somehow never hears Archie taking out his computer chips.