Great conversation, a few points.
1. Yes, it is great that because of the ideals of Starfleet, Hernandez transcended her abilities, survived, co-existed with a superior race in terms of their technology. Then she found a way to heal both the Borg and the decaying Caelier civilization, and make them a new culture again. Not only that, she won a debate within the superior race based on sound logical reasoning they could not refute. Bravo! The solution worked. And the idea of lost souls was brilliant. Great work by the author and his associates and editors.
As a Christian believer myself, I think it is a great solution. Redemption instead of punishment always works for me

it works for God (that is what Christianity is at its core)! But, the Caelier are not deity, and unlike our POV as readers, Picard does not have the option of knowing that everything will be all right at the end. So, time travel and thalaron radiation have to be on the table to be tried.
2. Under the circumstances, the highest authority that Picard serves under sanctioned him multiple times to do whatever it takes to win, and save the Allies. Therefore, as I understand military law and ethics, Picard was morally justified to build and use the weapon. The effects of that decision would be taken by the the Federation president and heads of Starfleet Command, even if they would have to fall on their own swords as a result. When the best minds the Allies had said this is the best the best solution, they should have used it, or planned to use it. However, winning sides have ignored advice before.
3. Picard IMO, had a duty to work for solutions on
multiple fronts, including all other ways to win this war, and in the main thread he was chided for not finding alternatives to the plan of Hernandez and Dax. If this was the best he had, well then, use it. the people who don't like the use of the radiation want it to be an either/or deal, and it can't be that. Picard should have (and did support Dax, and whatever Titan could come up with), and even make plans to try and scatter and escape the Borg if the Hernandez plan failed. Somebody on the command staffs in this little fleet had to or would be thinking about this-- after all "there are always possibilities," right?
4. With respect to those who are against the use of the Radiation weapon because it was illegal, please think about this probability. At least in the Romulan Empires, the moment they knew the Borg was coming in force that they could not stop conventionally, the radiation weapons would be put into use the moment they had them on ships. If Picard could make the weapon on a beat up starship, it is very logical to believe that anyone else with Federation tech or close to it would be using it, or close to using it. I mean, in this multicultural diverse word we live in,

can we not accept the fact that races different than the Federation would make different decisions than the high ethics of the Federation?
5. I think the ethical bounds of Starfleet are great here, work for a solution within the rules. But if it is a war of total extermination, which has never really happened in human history, then making it to another day gives you another chance to win. Where they were at the Radiation weapon was the last chance (other than what happened) for there to be a tomorrow, then it is immoral not to try and take the chance. As long as there is tomorrow, there is hope, even if hope is Q.
6. The problems with using the weapon:
a. It may not work: So what? You are losing anyway, and if it doesn't work, you lose. If you don't use it you lose. Where is the down side to total destruction?
b. It is temporary: Yes, be it 100 years, or two months. But the tactical situation can always change, even the strategic one. Many things can happen in two months or 100 years, with thousands of derelict Borg vessels floating around full of intel. For example, the Borg come back in 20 years, and run into Federation staffed Borg cubes filled with borg tech and new Federation tech. Well, can brute force win? Yes. Even if no solution is found, then you have time to evacuate the Federation, Memory Alpha, and and other allied world to any and everywhere, at least there is a better chance the civilization of the Federation survives somewhere.
c. It's illegal: So? The Breen are going to attack the Federation because they used the weapon? Why? Or should they not fear it for a while? And who among the Allies, the Gorn, Tholians, etc, are going to look at the carnage, and make war because it was used. If they had to, the Federation President could stand trial for war crimes if another group didn't like the use of them. Bacco would sacrifice herself for the Federation if she had to.
d. Nobody more powerful will help if you do use it: Well, maybe, but at that point if the Caelier can't or won't help it doesn't matter, Picard is dead. If some kind of other ST demiurge would or wouldn't intervene they would make a decision based on other or no other things, regardless of what one guy did with some weapon.
e. "Better to die with your principles intact": That is in essence what the person who brought up the non-violent types (i.e. Amish) say, and in many cases, I can agree. It is worth giving up your life for a cause (especially when there is something after death worth having, like eternal life!). However, as the people responsible for Billions and Trillions of lives, the leader of a state or military force is not able or allowed to make those decisions for all involved. If you are a head-of-state you are required to protect religious people, atheists, pacifists, and militarists, and use the power of a state to do it. that is why you are head-of-state. Martin Luther had some interesting things to say about this, if you are interested in such things. Even in the Mirror Universe episode, the people at issue is one society, on one planet, of one heritage and philosophy/religion. The whole Federation 125 years later is not. And to apply "the specific to the general" in this case is a logical fallacy in the argument.
Well, I have more to say, but my post is too long as it is. Thanks for Christopher's involvement in the thread, to hear a writer's views on the subject is a great addition to it. And thanks to all for reading my stuff.