1) You may not LIKE the fact that the intervention of extra-dimensional or extra-powerful entities is an option, but it is in the Star Trek universe and has been since the Organians told the Federates and the Klingons to get off their lawn. You may not find it realistic, but I find it no less realistic than transporters.
2) I hesitate to say that David Mack was trying to give the characters perfectly moral choices. I'd have to re-read the series with an eye to that question, but I would point to Mack's Vanguard series and to his novels A Time to Kill and A Time to Heal and The Sorrows of Empire as stories involving violent conflict and difficult moral choices that Mack has presented where no character walks away without some blood on his hands or some sin staining his soul. If one interprets Destiny as giving the characters perfectly moral choices, then that makes Destiny an outlier in Mack's body of work.
Yes, the Organians have been around since TOS. But they were almost never used since then.
Why?
For the same reason that technobabble shouldn't be used.
Because they give the characters an easy way out - no complications, moral or otherwise. One can't connect to such characters - because in the real world, such easy alternatives don't exist in life or death situations, and the viewer/reader instinctually knows this.
It makes Star Trek boring, uninspired, as some of the more sleep-inducing Voyager episodes prove.
Because they transform Star Trek into a cheesy children's tale.
That's why the Organians didn't enforce the treaty between the Federation and the Klingons. Our heroes had to find a solution themselves.
The occasional reset button or technobabble/higher being solution is fine, as long as it's confined to some forgotten episode.
Star Trek Destiny, though, should be this momentuous event in trekverse history. If televized, it could easily be an 12 episodes miniseries. It shouldn't have such a simplistic ending.
That not to say I didn't enjoy how David Mack presented the Caeliar. Some interesting concepts and I liked the imagery.

I disagree. The thalaron weapon was never able to stop the Borg. Even if (and that is a big if) it would have destroyed lots of Borg ships, it would not have saved humanity or all the other civilizations. All it would have done is making matters worse because it would make the Borg even more determined to exterminate the Federation.
If the Caeliar wouldn`t have wanted to help, that would have been the end.
I'm curious. How could the borg be more "determined to exterminate the Federation"?
They are already trying to end all life in the Alpha - and Beta - Quadrant. And they have sent an enormous number of ships to do that - 7400 - one for each densely populated world and significant space structure in the two quadrants.
Are they going to start twisting their moustaches? making threats? to start torturing their victims before killing them?
They can't send any more ships. Not for 70-100 years - Seven of Nine establishes that in "Mere Mortals".
As for the possible consequences of the thalaron weapon's use, i analysed them in detail in my above posts. If you are interested, I invite you to read them.
