Yes, you can do this. In fact the Incident Detector does this without any special conditions set by you. You can disconnect the "gfincoming" input from your Incident Detector and remove the "Active = true" from the conditions. Instead, configure your synchronization rule to have the "active" status of each geofence driven by a field in the source feature service like in the attached screenshot.
[ATTACH=CONFIG]26575[/ATTACH]
Any geofences that are pulled into GeoEvent Server will be active only if that field in the Feature Service was "true".
If you want to have that feature service populated by your "gfincoming" input, you can create an output that goes to the geofence feature service, and connect the "gfincoming" input to that new output.