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!
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The point is that any other option has a risk to it. If even one of the bee escapes, many will end up dying. Kiritsugu isn't the type to take that risk. One death to save many more lives is preferable to taking a risk to save them all. Blowing up the plane was the simplest solution to end it, no matter how you look at it. The longer the plane stayed, the higher chance a bee could escape, so the options you provided could have resulted in the death of thousands.