Disable Bluetooth on Apple keyboards and trackpad
If I open up Bluetooth preferences I can still see both of these
  devices listed.


Yes.  These are the Bluetooth devices that you system has remembered.  Just because they are listed doesn't mean they are connected.

If you want to remove a device, go into System Preferences -> Bluetooth, then select the device, right (or Option) click it, then select 
"Remove"




  I'd like to completely disable any Bluetooth communication and use usb
  as the only communication channel.


Turn off Bluetooth and plug in a USB keyboard/trackpad.

You can turn off Bluetooth by going to the same screen and clicking the button "Turn Bluetooth Off"

As for the keyboard and track pad, they are both Bluetooth 4.2 LE (Low Energy) devices.  This means they don't transmit anything unless they are paired (or pairing) with another device.  They sit in "listen mode" until it receives the signal to being broadcasting.  Basically, there's nothing to turn off.