The difference isn't obvious, especially since it has never been established that, if inserted into the Borg central consciousness, the geometrical shape actually would have destroyed the Borg.
But we do essentially know that in retrospect. Remember that part of the reason Picard didn't deploy the geometric paradox is because they now had a better "virus" to infect the Borg with -- individuality. We know from "Descent" that Hugh's individuality did infect his entire cube and turn its drones into individuals; in fact, when "Descent" aired, it was ambiguous whether it was just that one cube or the entire Collective that had been so transformed. But in retrospect it's become evident that it was just the one cube, and that the Collective presumably cut off contact to protect itself from the "infection." It follows that if the paradox had been deployed, its effects would've been similarly limited in scope.
Hmm. I think a case can be made that the paradox worked at a subtler level than Hugh's individuality--the one's pretty subtle next to the other which is a direct subversion of the core imperatives of the Collective--and so might have slipped by, but point.
Leaving aside the ethics, one major problem with genocidal tactics that aren't guaranteed to destroy a society is that they leave a serious risk is leaving the devastated society ready to respond in kind.
What would the Collective do if Picard in 2367 had inflicted very heavy damage on the Collective that fell short of destroying it? The events in Destiny
--a Borg reprioritization of the Federation as an existential threat requiring the destruction of the Federation and all its neighbours--would probably take place a decade earlier.
Janeway's destruction of the transwarp hub may have been problematic, but at least in doing so she closed down the more direct path between Borg and Federation space. Had the Caeliar's subspace corridors not existed, it's plausible that it would
have taken a century for the Borg to mount a counterstrike. In a century, the Federation and its neighbours could plausibly have been in a position to better resist the Borg. Even in Destiny
's time frame, had the Borg dispatched mere hundreds of cubes instead of thousands the local powers might have held their own, if at heavy cost. But in 2367?
If Picard had inserted the geometric paradox into the Borg collective consciousness, leaving aside questions of ethics he ran the risk of inflicting serious but not terminal damage on the Borg, in such a way that they would have had access to the transwarp corridors which led (in one case) within a light-year of Earth. Making the Federation stand out as an existential threat to the Borg at a time when the Federation was incapable of defending itself against a single cube would be a bad decision.