It isn't a 3% chance of a false negative, the 97% figure is conditioned on actually having HIV. The actual chance of a false negative is far lower, since most people don't have HIV at all.
I probably screwed something up, but in any case you are definitely right that the false-negative odds are very low among all potential applicants. Really makes the argument against seem foolish.
1) http://www.cbsnews.com/8301-504763_162-57333212-10391704/cdc...
2) http://www.organtransplants.org/understanding/marrow/
3) http://www.wolframalpha.com/input/?i=%28%281%2F20000%29++*+%...