Well, that sounds like a book.
But despite the failure, I'd point to Brexit as an example where there was a conflict that was still broadly speaking handled in a civilized manner. If I recall correctly, the EU never said that if the UK left, they would take steps to liquidate Parliament. It was (and is!) an acrimonious debate, but still a civilized one (contrary to apparently popular belief, "nice" and "civilized" are not synonyms and are at times diametrically opposed; at best "nice" is what can result from civilization, it is not the cause of civilization). And despite the fact Brexit narrowly passed, I guarantee that had the EU gone the route that Spain did, Brexit would not have narrowly passed, but passed by a wide margin.
Contrariwise, even with all of Spain's errors and provocations, by numbers it seems like Catalonian independence just barely has something like a majority, or narrowly misses a majority, despite the superficial voting numbers, and that I would imagine includes a lot of very squishy support. Let's call real support in the 40-60% range. Some emotional sweet talk in attempt to emphasize solidarity, combined with some threats about what "could" happen (both in terms of bad things that may happen economically and vague threats of retaliation from Spain) but with no actual violence threats, along with emphasizing that it is their choice ultimately, would probably have resulted in as much as a 2-1 defeat for the independence. If nothing else, even just an appeal to the status quo rather than the dangers of such a radical change has had some success as a political campaign ("don't change horses midstream" - relection slogan for Abraham Lincoln [1]). Convert that "squishy support" into "squishy rejection", and the numbers change a lot. I hope what I'm writing here makes it clear just how much of a wild-ass guess that is, rather than some sort of principled analysis; if your mileage varies, more power to you. My big claim is that it would have made the situation better moreso than the precise numbers.
That is an example. There were other approaches that would have done better. I'd also observe that the approach I'm proposing here strikes me as fairly European, with the emphasis on solidarity and such. I'm pretty sure I'd recommend a substantially different approach if we were discussing Texas secession.
I'd also point out that I'm not viewing successfully keeping Catalan in Spain as the end of history. The issues would still be there. "Something" would really have to be done about that. But all countries have stresses, and Quebec remains part of Canada to this day, for instance. The stresses don't have to explode.
(I've also read some analysis that suggests these actions would have been politically untenable for Spain's current leadership. So I'm talking about what Spain as a whole "should" have done, not what Spain's leadership necessarily could do. I still don't know where I fall in the "forces of history" vs. "big actors in history" debate, but I tend to think the answer is "yes, both by a lot".)
[1]: https://en.wikipedia.org/wiki/List_of_U.S._presidential_camp...