I believe you're missing the majority of your player's points. From what I've read, not even KJ disagrees that magic should be able to generate an apocalypse. The problem is that there is no in-between level of skill or magic.
To use the nuke analogy, you've trapped your players in a room with two objects: a butterknife and a recoilless rocket launcher. There is also an angry mutant cave bear in the room. What should they use to fend off the bear? If they choose the butterknife, you punish them because they just took butter to a bear fight. This is perfectly reasonable. If they choose the recoilless launcher, you punish them because they just set off a recoilless weapon in an enclosed space, not to mention the high-explosive payload. This is also perfectly reasonable. What is unreasonable is the fact that the player is only presented with the two options.
I think this kind of a game could work very well. A year or two ago I even briefly entertained the notion of a WOT game where the players were men who could channel, thus plunging them a little farther into uncontrollable madness every time they used their abilities. However, the players not only need to feel that there is another path than MAGIC, but that equal gains can be had from a path without MAGIC under 95% of all circumstances. More importantly, the chance of triggering a magical apocalypse needs to be small compared to the number of actions taken. Currently, you seem to trigger one on a 1,6. Which would be fine if there wasn't a 1/36 chance of that happening. Multiply by 6 players, who seem to be using magic at least half the time, and each turn gives you a ~10% chance to start the apocalypse. Far too frequent.
Well, that's my take on the situation. I'd love for you to cooperate.*
*I'd threaten to pluck out your eyes, but this isn't my thread. So the threats will be minimal.
Alright. What alternate solution do you propose? The dice only have so many sides, you know.
But that doesn't cover what we have. It's more like, when you have a hammer, a scalpel, and a loaf of bread and are told that you'll be destroying walls while the ceiling is falling. Sure you can do it with a lot of effort and skill with a scalpel but it's more efficient and less dangerous to use the hammer.
You have a lot more options than that, though. You're just not thinking well enough to use them.
You're also ignoring the helpful little careful casting rules.
((The biggest problem with mundane approaches to problems is the damnable skill system put in place, which basically ensures that everything mundane you do (aside from about two or three situations you may have predicted in your character sheet) is heavily penalized, essentially making mundane actions inefficient and unlikely to succeed 90% of the time, unlike magic, which works more often but with possible disruptive consequences (maybe institute a d6 apocalypse die that you roll when somebody rolls a 7-0, with a 1 meaning apocalyptic events and a 2-6 meaning regular destruction).))
For the first point: Only when skill would logically be a consequence. The alternative is to let anyone have a good chance of success the first time they attempt any kind of task, whether it's parkour or fencing.
For the second: Seems like a clunky obvious rules patch. Doesn't fit with the rest of the system.