Pad overlapping other device's pad
If there is only one connection on that net, then the simplest approach is to just hide the airwire. You can do this using the command:

ratsnest ! signalName


Where you replace signalName with the name of the net you want to hide. To make it visible again, simply omit the !.

The reason I say if there is only one connection is that if your wire was making up only part of a larger net, hiding the airwires for that net could hide a missing connection elsewhere on the board.



A neater approach would be to split the net up as you say, naming each end of the net. But then add an additional test pad to each end. There is a standard library called testpad which has single SMD or PTH pads. If you add one of these to each end of the net, and you can then attach the wire to this pad. If you don't have space, choose the smallest SMD pad option and place it on top of your existing pad in the layout.

To avoid getting overlap errors in this arrangement, you should set the "Clearance -> Same Signals -> Pad" and " -> SMD" settings in the DRC window to be 0. This will disable checking of overlapping pads.