Who knows what the real reasons were..
Pete Bethune had built the boat, had even taken a second mortgage on his house to finance it, but was considered a bit of a wild, "gung-ho", kind of guy, whose favourite phrase was "bring it on"..
He had always been the skipper of the boat, even in her Earthrace days, but Paul Watson was planning to make the co-pilot, Laurens de Groot, the skipper in the future, as he was a more level-headed fellow..
Maybe Pete did a kamikaze and stopped the boat when the Japanese whaler was approaching, suspecting the Japs would welcome the opportunity to run her over...
Rather than suffer the humiliation of handing over command of "his" boat, he scuttled her..
Just a theory..