This is an interesting post, but...
Hating Hitler doesn’t mean you’re biased against Hitler. Likewise, having a belief about a particular ethnic group doesn’t mean you’re biased for or against them.
Then how do you know what score you should get on the IAT? I don’t know what an unbiased score would be, but an equal-for-both-groups score is most likely biased.
In the Israel vs. Palestine case, your answer would depend more on some meta-level decisions than on ironing out another decimal point of bias. For instance: Should a settlement give equal benefits to both sides; should it compensate for historic injustices; should it maximize expected value for the participants; should it maximize expected value for the world?
If you want to maximize expected value for the world, you would end up calculating something like this:
Israelis have given us a hugely disproportionate number of the world’s famous scientists, musicians, artists, writers, producers, bankers, doctors, and lawyers.
Palestinians have given us a hugely disproportionate number of the world’s famous suicide bombers.
The answer you would then arrive at will be more different from the answer you would arrive at if “equitable outcome” is your goal, than the difference made by any bias. (Unless you really, really hate lawyers.)
So I don’t think this approach gets at any of the hard problems.
The Allies won World War 2 largely by killing about 2 to 4 million civilians in Germany and Japan. Therefore, it isn’t clear that the benefits of not killing civilians far outweigh the costs.
This will become more important as technology decreases the difficulty of building WMDs. Eventually, even a small nation like North Korea will be able to make nuclear missiles. By that time, the cost of allowing them to do as they please (and encouraging other nations to also do as they please) may be greater, in expected lives lost, than the cost of brutally killing a million North Korean civilians.
I would go on, but there’s no point in going to the next shock level.