If the borg had the capability to create grey goo that can eat planets in minuts, they would have used that capability before "before dishonor".
Not really. The Borg don't anticipate new problems. They can only react to those problems and invent solutions as the need arises. There are any number of potentials the Borg had that they failed to utilize because the possibility never occurred to them. This is something we've known about them since the very beginning, so it shouldn't be that hard to recognize.
The point is not that the cubes, denuded of their drones, will certainly develop the absorption adaptation. The point is that it is a very real, and very serious risk, and the negative potential consequences would be of such severity that they would outweigh the positive potential consequences.
Indeed. The point, more fundamentally, is that it's naive to assume that a thalaron weapon would undoubtedly
be successful at defeating the Borg. Even if the "denuded" cubes didn't develop that particular adaptation a second time, they would still be sentient technology driven by an imperative to destroy the Federation, so it is illogical to assume they would be rendered harmless. They might develop a different adaptation that would enable them to continue attacking the Federation.
If there's one thing the books leading up to (and including) Destiny
demonstrated, it's that you can't assume you know the Borg's limits. Every time it was believed they were defeated, they came back. Assuming that finding another thing to shoot at them would magically solve the problem forevermore is failing to learn the lesson of the prior sequence of events: that you can't beat the Borg with weapons. No matter what weapon you throw at them, they will always adapt. That's what they do. The only way to achieve a meaningful victory over the Borg was to change the very nature of the Borg.
So the thalaron weapon was not a magic bullet. It was just another false hope. Santayana said that the definition of insanity is repeating the same action and expecting different results. By acknowledging the failure of brute force and finding a better option, the heroes of Destiny
took the sane course. They rose above repeating the same endless conflict with the Borg and found a whole new paradigm for dealing with them, one that finally resolved the problem once and for all. I don't see how that can be seen as an undesirable outcome.