No it doesn't, it was made by the same production team telling a story about the same character which clarified that the whole plot of "I, Borg" was pointless and doomed to failure if implemented. It came later, but still clarified the whole thing.
Being individuals or a Collective didn't matter, the Klingons Romulans and Founder showed that they were the Feds enemies (for their time periods). The Borg can also be made into individuals, their Collective broken. There's little difference, an enemy is and enemy.
And yes, that they didn't bother thinking that it might be less than perfect IS a major flaw which made the episode not that well-done nor thought-provoking on the issues discussed (such as this one).
As it stands, we are just dancing the same old tune of whether the virus would work or not. I believe it wouldn't, you and ProtoAvatar believe it would. I see the big-picture, you see the small immediate scenario. I see billions saved, you see imaginary billions potentially killed (since the Borg never killed billions afterwards).