When and if they use it, we will be somewhat delayed while we realize "Hey, there's this new superflu that seems a lot like the one that Dutch guy came up with."
Except that the paper will already be there, so presumably he (at least) will be comparing novel H5N1 strains to what he came up with. On the other hand, the research has been done and the paper written. Presumably, several electronic copies exist in several locations, which means that the black hats could get their hands on it without too much trouble. So releasing the paper only makes it moderately less difficult for the black hats, but helps out the medical community.