If you dissable the "Standard Shipping" module, you'll lost your own defined shipping rates. The option my be there because you've another shipping module enabled but not configured.
I've had the same problem and disabling "Standard Shipping" module not only disables all my custom shiping rates, but it did NOT remove the option "Standard shipping" from purchase forms.
Finally I noticed that on "Configuration/Shipping" I've another shipping module enabled, that may be enabled by default after VM installation:
"Flex Shipping. Fixed shipping cost to set base value of order with percentage of total sale above base value"
I just disabled this one, and the "Standard shipping" disturbing option dissapeared.