That sounds like your basic rain sensor. The design of the typical rain sensor is to open the common wire connection when it has rained. That way, it doesn't matter how your controller works, when the sensor THINKS it has rained, your system doesn't water the grass.
Based on a brocure I could find online for the Greenkeeper 212, the sensor connection terminal is just there as an alternate way of installing a rain sensor without splicing the sensor into the common connection. So yes, as the others have said, you want to bypass the rain sensor all together (i.e. rather than connect common to rain sensor to valves, just connect the valves common wire directly to the controller).