I don't know if they would have stopped, but Rick and Daryl would have exchanged words. Given his reaction on the bridge when out with Merle, Daryl has become a big proponent of saving human life.
However Daryl would probably have deferred to Rick, but not without losing little respect for him.
Daryl's reaction on the bridge was because there was an infant in the car. I'm not so sure he would have stopped Merle from taking some supplies if only adults were in the car.