Leven Rambin receives her final on-screen credit, despite the fact that her character Riley doesn't appear in any new scenes. Her only presence is in an excerpt from a previous episode, of her first encounter in the future with Jesse.
Jesse orders the submarine crew to "abandon boat", not abandon ship. Sailors and Navies often display bigotry against small vessels. Ships are large and powerful, boats are small and weak. To any ship's crew, calling a ship a boat is insulting. From the 1860s to WWI naval types generally held submarines in contempt, dismissing them as novelty toy boats. After WWI subs sank a bunch of battleships they gained some respect; today submarines are still called boats, even by their own crews.
In the narrative behind why Jesse made John think Cameron killed Riley. Jesse was bent on destroying John's trust with Cameron by using Riley to manipulate John and making John and Sarah think Cameron was responsible for Riley's murder.