Select the rally point, and there should be a command bar on the bottom left to allow you to delete the rally point.

Find the rally point on the map, select it, and the command will be on the bottom right  You are right however, you should be able as well to delete the RP there, but that seems to be an oversight by the devs.

Ok, I understand your issue now, sorry I thought you were dealing with the rally point mechanic.  I havent played around much at all with the Govern-commands section.  Its very very poorly implemented IMO, having a few decent uses, but ship movements in this interface are by far too generalized.  Yes, I see you dont have an option to go back to the "unassigned" value, which is first present there.  You should certainly open a ticket on that, but hopefully they will ignore it as a new and better interface is hopefully coming soon.  Nevertheless, your ticket will add pressure to either fix it or implement a new design sooner than planned.