I've always seen catplosion and the resulting disinigration of your hardrive to be an end game scenario, removing this would be like removing (atleast one) of the final boss fights out of another game.
Just because an end game scenario is hard doesnt mean it should be removed.
The game is going to get actual endgame scenarios eventually. And I really don't think "run out of processing power so it becomes too slow, sluggishly-responsive, and boring to continue and you eventually quit in disgust" is really a desirable endgame scenario anyway...
It's not that cats make the game
hard. They add absolutely no difficulty to the game at all. In fact, they make it easier, because they constantly produce more cats that you can butcher for resources.
But they make the game
unfun, because things slow down to a crawl and the interface becomes too slugish to enjoy. Those are things that, optimally, should never happen.
I mean, look, if you like it, I believe you can force your game to lag and behave sluggishly using FPS caps. You can get as much 'challenge' as you like that way -- heck, you could push it all the way down to 1 fps in the late game if you really want! There's also various external tools you can use to limit the CPU available to Dwarf Fortress, simulating the lag of a catslopsion as much as you desire.
But I think it's fair to say that for everyone else, the game should be designed with, in general, keeping a high FPS as a goal.