I ran into a similar problem. There were some ant men on top of an inaccessible cliff overlooking my starting location. My miners didn't even grab their gear before running away from the wagon and got stuck in a similar "go grab pick, MONSTER!, run away, I still need my pick" loop.
Fortunately, there were a few workarounds. First, I drafted them so they could go grab their gear. Then I undrafted and let them start mining a little further away from where the ant men were.
Unfortunately, I ran into a new problem. I wasted enough time trying to figure things out that my dwarves had become thirsty and were stuck in a similar fetch/flee loop with the kegs. However, I used the new forbid option (WHICH ROCKS) to forbid the entire wagon and contents, and they happily drank from the nearby brook.
Finally, I tunneled to where the ant men were. Before I broke through, I grouped 6 of my 7 dwarves as a military squad and stationed them in the tunnel. Then I dug out the final square and quickly militarized the remaining miner. My dwarves charged the ant men and quickly knocked 2 of them off the edge of the cliff. The ant men flew a good 8-12 squares past the edge of the cliff before plummeting to the ground below. Didn't even receive a scratch.
Anyway, in your case, rather than turning off item hauling, you should just forbid the few items that're causing the dwarves trouble. You might want to also designate the area as a restricted traffic zone to minimize job cancellations and other grief. You might also be able to sneak a miner through there by tunneling underground before trying to come up through the cliff. Hopefully, the extra layer of rock will shield the miner from monster panic.