Well you have to remember that there was a massive evacuation prior to the Dominion attack. It makes perfect sense that non-essential personnel evacuated on the Runabout's while the remaining Starfleet personnel left on the Defiant and the Rotaran. That gives the slower Runabout's a head start to make it to a nearby starbase outside of Bajoran space. The Defiant and Rotaran would be packed for sure, but there's no reason why they couldn't offload personnel at another starbase after the evacuation.