Your problem was breaching the cavern before you were ready. If you hadn't invited the GCS into your fort it wouldn't have killed your dwarfs, it's that simple. A single carefully-placed hatch cover could have saved your fort.
See, I Didn't INVITE it, I didn't realise how it could get in the first place, I though I had every entrance sealed off. (Apparently i was wrong and never did find the hole I didn't seal, unless the GCS can scale walls now and I missed the update) Well, new fort going, I know I"ve got Iron waiting to happen (No Magma or Burn metals, so I'm running on Elf... er, Wood power, but I've dealt with this before.) ENTIRELY flat map, so I'm working on a palisade, had a hunter come in with his own supplies for once, so I know I'm not completely militarily boned if push comes to shove. (I know hunters are buggy as marksman, but something is better than nothing as I work on getting the real military set up.) Things are, looking alright.
Thank you DFhack, for taking an edge off the learning curve for people who aren't as good at this as they'd want to be. :3