Why is the OP talking about permanent claims, when his issue would be no different if the same missions granted regular claims instead?
Seems to me OP’s actual complaint is some combination of 1) Mission tree grants claims, and 2) Nations actually try to pursue their claims.
Because regular claims die off. Part of my problem is with mission trees and decisions creating railroaded results, yeah, but if they did it in a way that such things were temporary (i.e. with normal claims) then it wouldn't create this permanent vacuum of diplomacy around wherever those claims are.
You don't need to farm them to 100 trust. I've never been in a situation where I've lost an ally I cared about due to perma-claims if I kept relations over 100 and trust at or above 50. The guaranteed swap to Domineering if they get a PU is something else, but only the most basic of diplomatic massaging is required to keep them through permaclaims.
You need IIRC 90 Trust to stop them from randomly breaking the alliance. Part of the reason why alliances break is because all of a sudden they turn hostile with 'wants your provinces blah1, blah2, blah3, blah4... -260'.
My point is that they didn't want them before, then all of a sudden a million magical claims show up and they decide they'd like to shoot themselves in the foot by breaking the only alliance keeping them alive and turning hostile on their former ally. It's goofy behavior and actively undermines the AI who was operating more or less with a semblance of intelligence before the game decided to mind control them.
I'm sorry to say, but if your longterm ally was willing to turn on you because they got claims, no matter how many, they weren't on the best of terms with you to begin with. Allies with high trust and relations will last even if they do get claims. This is why you sometimes see the Ottomans paralyze themsleves by allying AQ, and remaining in a diplomatic deadlock until some diplomatic shennanigans occur that break it.
This reads like a 'git gud' post. I'm not complaining because it happened to me, I'm just stating this because I think it sucks for gameplay to have the AI do a 180 and decide they hate an ally all of a sudden because they have claims. It sucks whether I'm the recipient or the benefactor because, well, it just sucks. And if you've never been in the situation where that has occurred to you then consider yourself lucky I guess. But it happens to the player occasionally (especially if they don't know how Trust works and the magical threshold), and maybe more importantly it happens to AI alliances in every game. And let's face it, if anything this just creates yet another player advantage.
And I'm not sure what your definition of 'best of terms' is, but it's entirely possible -- and even probable -- to, for example have an alliance with two or three defensive wars togethers to keep each other alive and one party can still not have enough trust and decide they'd like to all of a sudden get eaten alive by their rivals because some claims showed up and told them it's time to commit diplomatic suicide.