I have not tried it, but it is possible / likely you can do this by cutting the power cable within the usb cable.
I would buy a cheap usb extension cable (male <-> female), and carefully cut it open (remove the outer plastic in the middle of the cable without damaging the wires inside).
If you are lucky, there'll be a red cable, and that red cable will be the +5V line - if not, you'll have to use a multimeter to test which cable is pin 1 / +5V / VCC (pinout here: http://pinouts.ws/usb-pinout.html ). Once you identify it, cut that cable (and only that cable!).
Then plug your iphone/ipod into your PC using your new cable, and the iphone will hopefully still work with the debugger but will no longer charge.
As an aside, I could imagine the possibility that bluetooth is automatically disabled (or switched to a lower power mode) when the battery gets low - in which case losing the connection may be inevitable. You could try asking apple support if they are aware of anything like that.