Another method is to leave holes in the board for the ICSP and jam a connector in. It's crude but will work for a few insertion of pins.
I've even seen it done wherever the engineer could find room for single pins, of course hooking it up took a cut up header with wires to a connector that the programmer could plug into. Dirty but it worked and if it failed you solder short pins in and use the other cable.
You can have the chips preprogrammed. There are adapters available that will let it plug into a programmer I think atmel either has those or can point you to them. If you do that it would be best if you did the programming and shipped them to the board house. Per piece prices for that or ouchy *if* they can even do it.
For one board house a company I was at shipped all the programming stuff to them and had an engineer go there and teach their people. There were several thousand chips to do so it actually was cost effective. It was still about 50 cents a chip which is stiff if you're doing 10,000.