An airplane flying through a thunderstorm has virtually no chance of being structurally damaged by a lightning strike. The lightning leaves a burn mark but nothing else.
The controller tells Nicole that "the altimeter will change position but try to keep the two lines even, even though they're not together anymore." This instrument is not the altimeter, but the Attitude Indicator or the Artificial Horizon. He is obviously referencing the Attitude Indicator since he had never told her where the altimeter was or what it looks like.
The controller tells Nicole to pull the controls back. He says "That will mean your wings are holding steady and that you are lowering the plane for landing." Without adjusting the throttles, this will cause the plane to start climbing and most likely would result in a power-on stall.
During final approach, there are no changes made to the throttles, flaps, or speed brake. IF she was able to land successfully, without staling, in the touchdown zone, it would be almost impossible for her to stop the plane before running off the end of the runway at that speed. He also never went over how to steer the plane once on the ground.
When Nicole is strapping the injured passengers in, the unconscious co-pilot moves his hand out of the way so she can secure the seat buckle.