As stated in the “Rain Sensors FAQ” article listed above, you really do not need to use a rain sensor if you do not want to. Rachio uses local weather stations (I suppose depending where you are) to understand the weather, more than just the precipitation.
The numbered list that I provided was in the Hunter owner’s manual in the first link that I included (see page 8). My interpretation is that when you are using an RS, Hunter has that hooked up to RS & C and you move the valve’s C to RS. Did that make sense? In other words, RS will have the sensor & valve C and C will have the other part of the sensor. I am not sure why that is.
So, if you do not use the RS, leave it disconnected and you will cap them when you are done. You will just have to figure out which of the wires is the actual valve C. If you have a multimeter, you can test the ohms between valve 1 and go through each of the wires (starting with the ones on RS and one at a time). You should read between 20 & 60 ohms if it is a valve. Otherwise, you probably will get 0 ohms if going from zone 1 to the actual sense.