I'd prefer not to pull apart my development board to program the SAM D10
One level down from 'pulling apart', is to just get at the sw lines of interest- the swclk, swdio and reset all have resistors in their path from the 32u4 so can be isolated. I'm not certain, but maybe just removing the swclk resistor, solder a wire on both pads to a spdt switch (in->sp, dt->on board, ext)- used to switch the swclk from either going to the on board sam or to an external sam. Probably won't look pretty, but we are talking about a $9 board that is meant to be used.
Or buy another $9 sam d10 mini board, remove the sam (or cut the traces close to the sam as needed) and use the swd connector- one development board, one dedicated programmer.
edit- a 3 pin header with a shunt would work just as good as a switch for selecting int/ext.
remove swclk resistor
mount 3 pin header
2 wires from resistor pads
cut trace near swd connector (bottom layer)
wire from 3 pin header to swd connector (bottom layer)
use shunt to select internal or external target
see attached picture
edit again-
I assumed the swd connector was populated, but I guess its not, so you could instead create your own 5 pin header (100mil) on the board close to that connector (vcc, gnd, A,B,C)- just connect to the 2 needed pins on the swd footprint (no need to cut swdclk trace), and 1 from the 3 pin header. It may be easier to deal with the standard header size, without having to populate that swd connector (50mil spacing).