Its an old question but there is a simpler answer
The nano probe technology in no way helped the Borg assimilate 8472, it only killed them. The Borg are not interested in killing them. 8472 were chased out of this galaxy and no longer a threat to the Borg, that's enough for now, so why go after technology to kill something that you may be able to assimilate later
The Borg don't kill the races they are interested in, they want them, but would rather wait until they CAN assimilate them than destroy them. The war was over, 8472 thought the humans were allied with the Borg (they weren't but it was enough to stop the war). 8472 was no threat to the Borg the moment they believed that humans would come to their aid, with this devastating technology. This is shown in a later episode where 8472 says 'the Borg are irrelevant it the humans we need to worry about'
So the simple answer is the weapon was useless to the Borg anyway, they needed to stop the war (which Voyager did) but they didn't want to kill them all, so there is no point in going after Voyager. You don't fire a missile at someone you want to incapacitate for the same reason (when your intention is not to kill). The threat the Humans now posed was enough to stop the war and they thought that the Humans and Borg were allies, so left the Borg alone
The threat of deleting the Doctor had nothing to do with it, as in that same episode the Borg told 7 to assimilate the ship anyway (and risk loosing the data they wanted, all they wanted was to stop the war)- even with that threat in place the Borg still tried to get the tech by force (but only to stop the war, which Voyager did for them by accidentally showing 8472 that they will side with the Borg). That is the whole story line of why 8472 were planning an invasion of Earth if needed (Voy: In the Flesh). They feared the Humans would come to the Borgs rescue and left the Borg alone because of that