Hmmm, interesting. I just had the dwarves come again and everything when without incident. I basically had them escorted the whole way by military and nothing ever started.
In the history of this fort, I only ever had one caravan arrive to big piles of bodies, because it couldn't be helped. They were humans and one of their wagons scuttled and they left, but there was no fighting.
What got me thinking though. Between the last human caravan that started fighting and the dwarf caravan that just went peacefully, I killed off my remaining cloistered weredwarf (coati I believe) and vampire. So they weren't there when the dwarfs came and things worked fine.
There's been seemingly weird stuff going on with loyalty and creatures. In the first dwarf caravan that started fighting, one of their hammerdwarves got caged and he was listed as a "merchant" in the unit screen. At some point, he changed to "friendly" and I released him and he wandered off the map, back to wherever he came from (Naked and missing both lower arms, I might add. That'll teach him to get rowdy in Presentgold!). The only thing that I can think of happening before I noticed he was listed as "friendly" was that my arena troll died. The odd thing about that was that this troll had seemingly been one of those "friendly" trolls that are getting more and more reported around here. But the original fight with the first dwarf caravan happened when one of my dwarfs wandered into the arena (my error there) when that troll was fighting a goblin. The dwarf started fighting the goblin along with the troll and that's when my military, that I had called to the arena, passed by the caravan and the original caravan fighting started. Did that troll somehow cause weird loyalty stuff?
With that troll, I could open the door to the arena after a fight and the dwarves would just come in and clean up while the troll wandered out the same door and got re-trapped. She would never fight with my dwarfs.