The fact that they were a "Secret" and Unknown to the UFP/StarFleet could've significantly altered history.
I can see your point with this, but then, you come up with the premise of having to explain how the UFP escaped assimilation/destruction in the alternate timeline from which Admiral Janeway originated from.
One possible explanation is the Borg haven't gotten around to executing their plan of sending hordes of cubes to Earth - there can be large periods of time between assimilation attempts (especially on the other side of the galaxy).
We also know that in the alternate timeline, Voyager took longer to get back, and Admiral Janeway mentioned she ran into the Borg a few more times - which may have kept the Borg's attention away from UFP in general and its possible the crew thwarted those invasion plans (somehow)... and because of those encounters, Janeway developed deployable armor and transphasic torpedoes (among other thing - which SF got thanks to Hypersubpace tech), it further helped to keep them at bay even if the Borg DID try to invade.
I suppose its also possible (likely even) her Voyager acquired intelligence about the TW hub and Borg activities from those encounters (it wouldn't be the first time because they already did something similar in 'Dark Frontier') which she relaid back to SF via Hypersubspace, helping them to shut down the TW exit aperture near Earth (and others in the AQ) - that would explain her knowledge of the hub she was taking VOY to in order to return the ship home sooner.
But, Admiral Janeway also pretty much shuts down Chakotay's proposal on taking VOY to the AQ and destroying the TW Hub from there, because there's nothing there apart from exit apertures - this kinda terminates the proposal that SF could terminate the TW conduits at their exit points even if they knew of their existence - but then, Voyager DID manage to collapse a TW conduit in Dark Frontier with about 4 Photon Torpedoes (although that was the one created by the Delta Flyer when they left from VOY to rescue 7 of 9 - which could mean you can collapse the conduit at its point of origin, but not its exit aperture).
If that's the case, then Voyager in the original timeline may have ended up going on a mission to a Borg installation in the Beta Quadrant to thwart the invasion of Earth and UFP before they got back... who knows.
It could have been a combination of efforts... VOY encountered the Borg a few times, developed tactical systems, the Borg 'may' have attempted to invade Earth, but got thwarted with a defensive fleet which was armed with Transphasic torpedoes and ablative armor - so they were able to deteer the Borg thanks to VOY's efforts.
We don't know when the Transphasic torpedoes or ablative armor were devloped though, so its difficult to determine the exact sequence of events or when a potential invasion could take plece - but its possible VOY was simply keeping the Borg's attention away from UFP in the original timeline - and despite all the crewmen who died... maybe that future was better from canon point of view for the UFP.
Although, in that original timeline, the TW hub is alluded that it still exists (nothing was mentioned it was destroyed - otherwise, it would probably be mentioned).
So, who knows if the new timeline is actually better. On one hand VOY got the future tech and possibly the database from admiral Janeway's shuttle which would have given the prime timeline better chances in the long run... on the other hand, the original timeline UFP is able to keep the Borg at bay because of different sequences of events, but the Hub still exists (as does the Queen perhaps?).
With the destruction of main unicomplex (the heart of the Collective), its very conceivable the Borg wouldn't be able to recover as easily as it was suggested in the novels. Destroying the queen at remote ships away from Unimatrix 1 is relatively simple and she can just respawn at the unicomplex... but what happens when you infect the queen while she's at the unicomplex which also ends up obliterated along with the TW network?