, muddy that floor, never use the clean command again to help with fps, or else have to remud the floor again,
Nah. Once the farm is built, it stays built; clean away.
Alternatively, you could obsidian cast on that level and then dig away the resulting wall to restore the natural floor layer. Or on the level below, and then build and deconstruct a floor on top of obsidian floor.
If your literally entire fort died and all your food was lost because of a single cave-in, you all but deliberately engineered it (there have been several megaprojects based on linking the fort to a single support, or bringing the sky through it - though caveins don't go through stairs, so that requires bit of planning. )
But I don't think so. Butcher some animals or gather some plants from underground, turn on all medical labours on all uninjured dwarves - or alternatively, remove the hospital if treatment is not possible/you need their labor and they can work.
Even if only a single dwarf survived, you'll be back up to over 80 dwarves in like two to three years with immigration, more with visitors. Hardly fort-ending, though redoing work is never pleasant.
Now, if the fire was caused by you releasing clowns into the sky, you might have a fun challenge to go with that. In that case, setting up safe bunker would be first priority, lest they pour through the hole and kill everybody - and after that, would have to carefully distract/capture them and/or construct migrant entrances.