They weren't supposed to be isolated, though - that was just the unfortunate outcome when the experiment failed.
The difference would seem to be that this was legal genetic enhancing, and potential Khans could have been spotted early on. The likes of Julian Bashir are cases of illegal genetic enhancing, which by definition cannot be controlled and potential Khans weeded out.
Why the government would refuse to do controlled therapy on the Julian Bashirs of the world when it conducts research on the subject anyway, we aren't told. But the point could well be that Bashir never really needed any treatment and could have lived a happy life just as is. The type of therapy his parents wanted had a high potential for new Khans and little merit otherwise, and the folks at Darwin were in fact searching for better therapies with more controlled and more beneficial results.