When the turntable was operating, the rafts were not stopped. See the disney grizzly rapids video I posted above for an idea of how they did they.
Once the turntable was switched off, there would have been a steel panel, hinged on the floor, with a hydraulic or pneumatic ram attached to it that would move sideways - towards and away from the loading platform. When the raft was in the correct position, the operator would engage the ram, which would sandwich the raft between the station and the ram, keeping it wedged whilst guests were loaded \ unloaded.
Although this kept the raft in position, as a single pivot point, loading on an angle (if the gap didn't line up properly) would cause the rafts to wobble a little - which is why (i think) the rails were installed under the water in the station, to prevent the rafts from tilting much under the shifting weight.
I think both Australian rapids rides had similar issue with the turntable - in a risk averse world, there was too great a risk of someone falling into the water with a moving platform and a moving raft. By stopping both, it was deemed 'safer' - but because stopping rafts increased chances of collision, other control measures were needed to maintain safety. By all accounts it sounds like Wonderland did, and Dreamworld didn't manage those control measures effectively.
I can't speak for dreamworld, but in the rotating turntable days at wonderland, usually - guests would simply be sent on another round, and the turntable would only be stopped in a serious emergency. In other words if a guest was taking too long to get in \ out, the ride would not be stopped, and they'd be instructed to stay on \ stay off and wait for the next one.
The turntable could be stopped, but that would muck up the spacing for the entire ride, so would only ever be done for an emergency.