@dbrook: common off-the-shelf rain sensors are basically rain-activated switches. OpenSprinkler’s firmware handles rain sensor in the following way: if the ‘Use RainSensor’ option is turned on, and if the rain sensor is activated (this depends on the rain sensor type, either normally open or normally closed), then it disables all stations until the rain sensor is deactivated. In the situation you described, it will stop stations in the middle of a program, before the last station is completed.
Since the behavior of the rain sensor is implemented in software, you can modify the source code to implement any way you want.