I agree that their method for bringing down the collective was quite far fetched, especially postulating that Hugh's new found sense of individuality would wreak havoc on the Borg (aren't all drones individuals before assimilation?) but overall I think it was a brilliant episode. I just watched this episode recently actually and I'm still surprised the Borg even bothered to come back to fetch Hugh and the components from the other drones.
The way they took the most dangerous and hated enemy of the Federation and tore down the assumptions and prejudices of the crew was interesting to watch. They even set up wise old Guinan with these preconceived seemingly unwavering ideas of who the Borg are, and by the end of the episode she was up to bat for Hugh. I think this episode works because it says a lot about knowing one's enemy and the own prejudices we hold. This episode gave the crew (and audience) an interesting insight into loneliness as well.
I have to admit the other thing I didn't like about this episode was Dr Crusher. Yes she's taken the Hippocratic oath and is committed to healing individuals but her incessant holier than thou attitude in this episode didn't sit well with me. It felt like the writers were just using her as a lazy way to bring up conflict instead of bringing it out from the plot. I can see her wanting to bring Hugh on to the ship when they found him, that fits with her character. But the scene that gets me is the one where they are sitting in the observation lounge and discussing implementing the virus and she asks "Isn't this genocide?" which launches a very unnatural feeling speech where Captain Picard defends his position that the Borg as a collective are not innocent. I feel like maybe that discussion would have worked a bit better either later on in the episode OR if maybe she wasn't the only one who was questioning the validity of their plan at that point.
I don't think this episode negates the Captain's feelings about the Borg as a collective or organization. His experience with one briefly liberated borg drone does not erase the trauma he faced when he was forced to act as a member of the collective to eradicate humanity.