This has been interesting to chew on. Let me say that if there are actually delays, obviously those impose other costs (as a sister post explains here) and so the cost-benefit calculation may come out differently. But your original post was only about whether it's worth risking lives to avoid lurching trains, which is why I thought it was interesting.
I think the problem with your cost-benefit analysis is that you are using different methodologies to value the cost and the benefit. If you value the benefit of non-lurching trains by asking what people would pay, then you need to use a value for human life that asks what people would agree to receive to be killed--which I believe is much more than $6 million.
Conversely, if you are going to value a human life based on lost earnings/support to family/etc., or some other figure which might produce results in the ballpark of $6 million, then on the other side you need to consider only the lost earnings/hard economic costs of an annoying train ride, which are $0 -- there is no economic loss caused by lurching into a station.