The agent was designed to have a long incubation period so that it could spread pretty far through the Collective undetected before actually doing any damage. Since they wouldn't have noticed it was infecting them, they wouldn't have adapted to stop its spread. Of course, if Leybenzon had succeeded, it would've probably only shut down the one cube, since they didn't have time in that emergency situation to let it spread gradually, and probably shortened its incubation period considerably. That was the problem with it -- it was more a long-term weapon than an immediate defense. But it was all they had at that point. The ultimate challenges in Star Trek have always been the exploration of the universe and the quest to improve ourselves.