This question came about in Endgame when the Transwarp Hub was destroyed. Apparently there are 6 Transwarp Hubs in the galaxy and each one standing by with a Borg complex and millions of drones. This implies only a Transwarp Hub was destroyed and the general facilities that kept the queen. Whether it is possible to cripple the Borg using the same nano-probe type infections is being debated. It is also true if the Borg isn't stopped they will use their technology to conquer the galaxy.
Their are loop-holes concerning the Borg but an unnecessary loop-hole is what happend after the TransWarp Hub was destroyed.