Because it's real or as they stated the carts run off and you will have to reorganize to move forward? I don't know but honestly if caravan guards did their job correctly they would stop the menace from getting close enough to scare the chocobo's away and the caravan can keep moving. I know this is a irl scenario but caravan's don't keep moving when they are under attack and leave their guard behind, because they might be going into a trap where everything will be lost.

edit: also the fact that if it kept moving and took you awhile to kill the attackers then you would have to hunt down where the caravan went to and catch up... so that's why they have them stop so it is at the pace of the player, or party.