There is no JUSTIFIABLE reason for Kiritsugu to blow up that plane just yet. He could have had Natalia pilot the plane into the water, had her escape and then blow the plane up. He could have had her jump [i]OUT OF[/i] the plane and had some sort of cushion underneath for her land safely. No matter how you look at it, blowing it up right then and there is absolutely retarded.
HAPPY -blam!-ING MOTHERS DAY KIRITSUGU!
-
They had to establish him as someone who can get shit done no matter what. It worked.