Why does Automator need the discrete GPU?
Some of the Automator actions, such as those pertaining to Quartz, use the discrete GPU (if available). It may be a stability thing to require the discrete GPU on launch (similar to VMware Fusion). If you regularly use Automator and don't use the Quartz filters (or don't care about the performance gain) it should be safe to use gfxCardStatus. Just select Integrated Only before launching Automator.