I did modify my Crucible code so that the effect starts slow and gets stronger with time. I have the number of mana sources destroyed or spell spheres removed ech turn based on a random number up to 1/7th of the number of turns it has been since the wonder was completed. In my test games so far, that tends to mean you are unlike to notice much for the first 20 turns but all the world's mana is destroyed within about 75 turns and no units are left able to use any magic within about a hundred turns.
Originally I coded it so that it eliminated unimproved mana first, then nodes, and then unique features, but I think the code is simpler and more elegant if they are all treated the same (except only ordinary nodes disappear with the bonus itself).
Now I just have it first eliminate mana from the map, then from cities, and then start taking promotions away from units. It starts with archmage level promotions, then mage level, then adept level, then buffs, then finally starts destroying equipment.
I'm thinking of also causing the Crucible to cause newly trained arcane units to begin without their highest level channeling promotion, so mages become de facto adepts and archmages are basically mages. The existence of the Crucible would also stop adepts from getting their free civ-specific spell spheres which normally don't require mana..
I'm also thinking of it making Elementals, the Undead, Angels, Demons, and Golems start out weak, and having it start killing those units outright once all the other magic is gone from the world.
Originally I was thinking of the Crucible as primarily a technological machine of industry that just happened to inefficiently use mana as its power source, but now I'm thinking of it in more the metaphorical sense of a device designed to refine a crude ore by separating out all the impurities. I'm thinking its original purpose was likely to cleanse the world of the taint of hell still left behind after the reconquest of the Fane of the Lessers. It might not be primarily anti-magic, but anti-Armageddon. I'm thinking of making it reduce the Armageddon Counter each turn by just as much as it reduces the world's mana supply. Maybe Righteousness would be a more appropriate tech prereq, or an additional one.
How attached are you to the idea of effects being permanent? Would it be better if razing the city where the wonder is located reverses the effect?
I originally said permanent because I didn't think it would be possible to restore the mana from buildings accurately, but I think I've figured it out. Restoring mana granted by unique features is fairly simple if the improvements themselves stay on the map the whole time.
I think I could use the temp bonus feature without an actual temp timer to store the data of regular mana sources (and similar the temp improvements feature to store the nodes ), but if something else changed a counter it could mess stuff up. I think changing the normal bonus or improvement might clear the temp one too, so building a farm and then discovering wheat or something there could permanently eliminate a mana node. (I definitely would not want to risk losing unique features through such a method.)
It is probably not worth restoring ordinary mana sources on the map at all, as The Rites of Oghma can make up for their loss.