How to set throttle to zero even if RTL is enabled on ground

On our last flight we had to land the plane a good 400m from the launching area. The plane landed in manual mode but once it was on the ground, the receiver/transmitter connection was cut and the receiver set the Arduplane to RTL. That started the engine which could not turn due to being on the ground and by the time I got to the plane, the motor burnt out.

So How can I make the APM aware of being on the ground so it does not engage the engine, regardless of the flight mode?

I have also encountered the same situation as you mention.
Though it’s a common practice to keep the transmitter whole time on during the autopilot board get power, but some time or some one will not follow this rule.
With the RTL mode at ground, most often there’s no harm when landed near launch position but if the relative altitude is drifted up to 10M(very likely) then the motor will suddenly spin without any warning.
This is a very dangerous behavior when it happens people might get hurt.
To prevent this, as my opinion, should not enter the fail safe state if the previous throttle value is at low throttle(on the contrary to normal throttle to fail safe throttle).

As i know, issue the GCS MAV_CMD_COMPONENT_ARM_DISARM command is the only way to disarm the motor from arming sate, maybe can put the same logic to disarm control - lower the throttle to minimal then turn off the transmitter.