Destroying all the Flood in our galaxy is a temporary victory/solution. We know that the Flood came from outside our galaxy, so killing all the immediate Flood threats is not a final solution, just a setback. The Librarian knew this and therefore knew that that the Flood threat could resurface. To ensure a true victory Flood samples needed to be kept and studied to come up with a cure, one which would properly and ultimately defeat the Flood. Hence why she proposed to keep samples.