Similarly, in 'Endgame', Janeway had to choose between two options:
- either destroy the transwarp hub, immobilising the borg for, at most, a few years (at most because the borg, with unlimited man-power, could rebuild the transwarp hub; or it could build slip-stream ships; etc), after which time the federation was to be destroyed by the borg (the federation having no chance in hell of stopping even a smallish borg attack - as seen in 'destiny')
- or don't destroy the transwarp hub, keeping the federation a low priority target for the borg, the borg concentrating on other species.
In other words, Janeway had the choice between her peeople and stangers - another situation in which there was no morally 'white' option.
Janeway chose to sacrifice her own people, federation citizens she was sworn to protect - thus betraying her oath as a starfleet officer, to be loyal to the federation.
I'm not going to get into the Picard thing because it's not my particular area of expertise, though I don't find your argument in the least bit compelling.
Regarding Voyager, Janeway and Endgame, however...
While you may find the writing of Engame a little shortsighted, the case as portrayed in the episode was quite clear...
Yes, the Borg had assimilated slipstream previously, but Seven told Janeway (I think in Timeless) that the Borg had abandoned slipstream because they found transwarp more efficient. Could they go back to it if they needed to? I guess. But transwarp was their standard means of FTL propulsion at the time the episode aired.
Janeway chose not to simply use the hub to get her crew home early but to destroy it because as one of only six hubs in the entire galaxy it was believed that to destroy it, rather than use it, would cripple the Borg and prevent them from assimilating lots of people who otherwise might have been assimilated. And the hub was only part of it. The hub was merely a juncture for the transwarp tunnels which were also destroyed in Voyager's attack. The hub the Borg could rebuild, but the transwarp tunnels themselves...I'm not sure we have anything in cannon telling us how those are created...if the Borg did that, or just found them and put them to use.
In the episode Janeway asks her crew to weigh in on using versus destroying the hub and all of them agree that to spare billions of people they don't even know possible assimilation, it is worth extending their journey as long as it takes. Tuvok is facing a mentally debilitating illness and Seven a possible death, but all agree to risk that to seriously hinder the Borg's ability to assimilate others at will.
It is only once that choice is made that Janeway and the Admiral concoct the idea to further cripple the Borg by infecting the Queen with a neurolytic pathogen that will kill her and do heaven knows how much further damage to the collective to create the possibility that Voyager can have their cake and eat it too...destroy the hub, and get home in the process.
At no time is the point raised that by doing this, they are going to so totally piss the Borg off that they will direct all of their efforts to ending the Federation. The Borg have known about the Federation, and presumably had those transwarp hubs leading to the Alpha Quadrant for a long time already. Voyager has also seen firsthand that sometimes the Borg shoot themselves in the foot, as with Species 8472 so to decide that the Borg are completely unstoppable would fly in the face of Voyager's experience with the Borg.
You may think that the characters could not have thought otherwise...surely if we do this the Borg will destroy the Federation so maybe we should reconsider how much we want to piss them off...but that was not the argument made in the episode. Janeway's intention was to deal what she believed was a crushing blow to a species that was obviously incredibly dangerous, and for all she knew close off a number of a handful of routes they had all over the galaxy, including to the Alpha Quadrant. She was willing to sacrifice herself, her crew, and their chance to return home early to do that, potentially sparing billions assimilation and but for Admiral Janeway's choice to sacrifice her life in the final attack on the Borg, would have done just that.
You are taking what you would have thought in their place and perhaps what eventually occurred in Destiny as evidence that our characters are criminally negligent or criminally stupid or both. But the idea that this action might have greater ramifications for the Federation in the near future was never on the table here.
But for a moment, let's say, they had thought of it. Let's say Janeway decides that this action, in addition to sparing those who would have been assimilated using this hub, will so enrage the Borg that the Federation will now become the sole target for the Borg. Yes, we saw in Destiny how much trouble the Federation had dealing with the attack. But Janeway would have had faith in the Federation that you obviously do not share. If the Borg are fighting the Federation, they also aren't off assimilating others. I'm pretty sure Janeway would have believed that whatever the Borg threw at them, the Federation would find a way to counter. She'd done it on her own a number of times already in their battles in the Delta Quadrant. So yes, she's putting the Federation at risk, but at a calculated risk she would have believed the Federation would have been in a better place to handle than alot of other civilizations. Further, if we accept your premise that the Borg already have a route to the Alpha Quadrant, be it the transwarp tunnels or going back to slipstream propulsion, it is only a matter of time before the Borg come for the Federation so either way, what's the difference? The Federation knows the Borg will come eventually. Presumabely they are preparing for it, and for Voyager to return at this point with all they have learned in their years of fighting the Borg, they might be bringing information the Federation can use in their ultimate showdown.
When you are talking about the Borg, you are talking about a species that is going to do damage wherever they go. Janeway didn't have a choice to end them forever, but she had what she believed was the next best thing and she was willing to take it, no matter what sacrifices it would have demanded of her crew.
I just don't think you can judge the Janeway of Endgame by the fallout of Destiny.
Probably just me.