After triggering the Twilit Kargaroc cutscene, wait for the Twilit Bulblin to stop firing arrows at you. Turn into a human and make sure that the Kargaroc is coming after you. Get into the water and put on the iron boots to sink down in the water. When the Kargaroc tries to follow you into the water, it will kill the Bulblin allowing you to immediately head up Zora's River.
After warping the huge lava rock to Zora's Domain, head behind one of the walls and turn into a human. Run over and jump into the water, using the iron boots to sink below the submerged arch and head down river. This will skip hitting the trigger that activates the cutscene.