1) I'll never understand this opposition to using the Thalaron weapon. If the story needed it not to work, then it wouldn't work (same thing drives me crazy about I, Borg)... it's that simple. But for our heroes to not even make an attempt to save their civilization is weak.
Again, the key is recognizing that stories are driven by character, not just plots and events. The thalaron controversy was a means to explore Picard's character, to show how far gone he was into darkness that he was willing to embrace the evil that had taken Data's life and use it in a futile, childish attempt to strike back at the bad people who'd hurt him. That plotline wasn't about the weapon or the technology or the military logistics. Those were just background, means to the real end. That plotline was about two human beings, Jean-Luc Picard and Geordi La Forge, and their emotions and relationships. It was about Picard almost giving in to the ugliness his Borg abusers had left in him and Geordi pulling him back from the brink.
And the problem is - this controversy makes NO sense - morally and practically.
Meaning, by our perspective, using thalaron weapons in self defense against genocidal invaders IS moral.
AND, also, from the 24th century perspective, the actions our heroes undertook in 'Destiny' alone show using thalaron weapons against genocidal invaders is 'moral':
"The thalaron weapon was immoral because it would kill borg drones? Well, starfleet did their defeatist best to do just that throughout the books.
Or was it immoral because it could destroy all life on a planet? Standard foton torpedos can do the same thing equally well - indeed, an atmosphere assures nearly 100% antimatter annihilation (meaning foton torpedoes are quite effective when it comes to planetary destruction)."
Also - there's nothing 'futile', 'childish' or 'ugly' in using a weapon that has excellent chances of working against the borg -
as per 7 of 9 - in order to stop or delay the collective from killing TRILLIONS.
2) It's silly to have a moral problem with one type of weapon of mass destruction (thalaron radiation) but have no problem using another (transphasic torpedoes) weapon from the future which they also have laws against (Temporal Prime Directive), which cracked Borg cubes like walnuts. It shows an inconsistent application of Federation "morals".'
Not at all, because a transphasic torpedo isn't a weapon of mass destruction per se. It's a very targeted kind of tactical weapon, not more destructive per se than an ordinary torpedo, just better at penetrating Borg defenses, harder for them to adapt to. It's a surgical weapon, one specifically invented to counteract the Borg's ability to adapt. There's just no comparison to something like a thalaron weapon, which is like a neutron bomb on a planetary scale, something that can wipe out all life on an entire world while leaving the structures and technology intact. Just imagine if that technology got out and into the hands of conquering powers. It's absurdly naive to argue that the Federation would be
safer in a world where thalaron technology became widely known.
A 'standard' foton torpedo IS a weapon of mass destruction. It's has a matter-antimatter warhead, ideal for extinguishing all life on a planet in minutes. It's just as bad as a thalaron weapon.
Also - "Just imagine if that technology got out and into the hands of conquering powers."

What 'conquering powers'? The only thing remaining after the borg are done with the alpha/beta quadrants will be ash clouds.
Worrying about the external politics of ash clouds is ridiculous.
That's the absolute worst case scenario - far worse than thalaron weapon proliferation.
At that point, the federation should have prayed that it will survive to worry about thalaron proliferation.
She asserted her independence, took charge of her life, took action to discover the key to resolving a horrible crisis, and then persuaded the Caeliar to admit their mistakes and act to resolve them. It wasn't the Caeliar who saved the day, it was Erika Hernandez. An ordinary human captain who went through an unimaginable ordeal, managed to survive and adapt against all odds, almost lost her humanity in the process, but ultimately reclaimed it while becoming something greater, and thereby reached the most beneficial solution for all concerned. It doesn't get more humanistic than that.
Thematically and story-wise, Hernandez was a half-divine being, a 'Jesus' figure.
She may have been human hundreds of years ago - by the 24th century she was more than that, she was beyond human - and, at the end of the books, she achieved full divinity, she became a 'god of night', a caeliar.
Humans - the federation - played no significant role in their deliverance (beyond being a taxi service for Hernandez).