Based on how difficult it is to get into the TCM, you'd be best off splicing a switch into the heater or just disconnecting it entirely when not needed.
You could also tap something like a CANDue into your CAN bus and have it resend your preferred heater command each time the car starts. Now that I have the Arduino in place for CHAdeMO, I've been thinking of having it modify a few things like this - watch for the recirc to turn off and turn it right back on.
I might add a new control for the seat heaters (I don't think they are controlled on CAN) so they don't turn on unless the temp is below a certain threshold or add a stand-alone interlock circuit that turns them on/off with a momentary contact switch - but defaults them to off when the car starts locally and on when it's started remote and plugged in.
Maybe something that would mute the stereo when it can't connect to my Bluetooth or when I disconnect from USB audio...