The point isn't that every urban intervention should be corrected and replaced. Since the 1950s, we've learned a little about what works and what doesn't. The Prado was a fairly intimate intervention; it was a dangerous precedent, but it was also a limited one, and it would be mistaken to think that it necessarily endorsed a slippery slope to gargantuan spaces like City Hall Plaza (and what should more accurately be called the Rose Kennedy Plaza or Highway). It would be like saying "well, you liked Hausmann's boulevards, so why not Moses' freeways?" That would have been a legitimate intellectual trap in 1965, when planners thought they were participating in the same tradition of demolition and reconstruction, but I think we can see the difference today.
In fact, if I were in charge of rebuilding the space atop the Artery the Prado would have been one of my models of a successful public space to incorporate into the new street grid.