It turns out he does take a knife to Ned's throat, but it isn't just a random knife, and he isn't doing it do hold Ned down or something. Instead he took the dagger that Ned was wearing, that was used in the attempt to kill Bran, and smiled apologetically at Ned as he said his line. So instead of it being a purely malicious act further showing Littlefinger's archvillain status, as in the show, it is him reclaiming his own dagger and kinda lording his power over Ned. Similar actions, I suppose, but the character is portrayed entirely differently.