We might note that the Sphere that carried our heroes home evidently survived the virus attack (but not the indigestion caused by the Voyager). Much of the Collective would be similarly physically separated from the Queen; whatever software blocks were in place would be crucial for the ultimate outcome.
On the other hand, Admiral Janeway says she injected "just enough" of the virus to "bring chaos to order", which is difficult to interpret as anything else but admission that total destruction was neither the goal nor the likely result.
Seven of Nine ultimately says that "the transwarp network has been obliterated", which may be a truthful and accurate statement, but need not indicate any permanence. That's the degree of devastation actually established, though, apart from the Delta Hub blowing up.
Timo Saloniemi