At one point in the episode, they came up with a plan for destroying the transwarp hub; which would involve using a torpedo from within it, and then quickly leaving to outrun the shock wave. This plan would leave them still stranded in the delta quadrant, presumably because they would have to leave the hub before they could get to a part of it that would take them home. From Memory Alpha:
Tuvok and Seven put forward an idea: the use of transphasic torpedoes, fired from inside one of the conduits, programmed to detonate all at once. This should cause a cascading collapse of all the conduits, destroying the hub. The Queen would not be able to stop it. However, to avoid the massive shock wave from the explosion, Voyager would have to get out of the hub in ten seconds.
Later, Captain Janeway and Admiral Janeway discuss the possibility of using the hub to get home while still destroying it. We eventually see that at least part of their plan was for Admiral Janeway to inject herself with the pathogen so that when she was assimilated, the Borg would be destroyed.
My question is; how did infecting the Borg in this way allow them to use the hub while also destroying it? If they had the ability to outrun the shock wave long enough to escape into the Alpha Quadrant, then why wasn't this always their plan? Why was infecting the Borg a necessary part of this? Ultimately, what was the plan that allowed them to both destroy the hub and use it to get home?
I am assuming that getting "captured" by the sphere and going home inside it wasn't part of the plan all along; as they never could have predicted that sequence of events. But even if they had; I don't think this addresses the question.