What I'm saying is one step further, and more unreasonable: that if the disability disqualifies the person, then the government should compensate them for the marginal loss in wages that they could have earned from that job if they were not disabled (against a lower-paying job that they are still qualified for).

The ADA only prevents discrimination by employers against disabled people where the disability does not disqualify them from the job.

> Wouldn’t that undermine the fact that people with disabilities shouldn’t be evaluated based on their disability and ‘reasonable’ accommodations should be made?

This is a good general rule of thumb for the everyday treatment of the disabled, in terms of integrating with society. But I think this is insufficient to bring justice to the disabled. But you have a point and I guess the following may be a better way: with respect to disabilities arising from government service, there is a point in time when the government's actions have caused an individual to be disabled. Thus the disabled individual may be compensated for the amortized future loss in wages at one go; thereafter the law should not actively discriminate (positively/negatively) the disabled based on their disability. If a society should then decide to be more magnanimous, this may be done, too, to the naturally disabled, once they become of age. (not while they are too young, or this would create a perverse incentive)