How do I plan for in circuit programming of an AVR?

I've used ISP for just about every AVR board I've done; it's nothing to be afraid of. The AVR ISP mkII manual gives a pretty good summary of the limitations you need to look out for in the "Target Interface" section. Basically, if you run the MISO/MOSI/SCK pins directly to the programmer and have about 820 ohms between them and the rest of the circuit (and aren't doing anything funky with the reset pin) you're okay. I wouldn't worry about the ISP damaging other components; it's not a high voltage programmer. The signals all run at 5V, so if it can damage an external component, so can your microcontroller.

If you're really stuck with a board that doesn't permit ISP programming, I'd at least try to use a ZIF socket for your programming board. They're pricey, but it will greatly improve your quality of life.