I happened to think about the Raspberry Pi. On the model B, I was able to cause a reset by removing the WiFi USB dongle. But for the B+, they added additional circuitry to mitigate this. What was it? The AP2331. The device is simplicity itself. It's an SO23-3 with pins for in, out and ground. It was designed for USB power applications, but it's usable at 3.3 volts as well, which makes it ideal for my purposes.
I tested one using pin clips to attach it to my current revision of board, making it the bridge between the 3.3 volt and target power pins of the jumper block, and pulling ground from the controller. Without it in place, I could cause glitches on the controller fairly consistently with a pogo adapter and a Crazy Clock board. But with the device in place? Nothing. It just worked.
So I'll be adding one to the 0.5 version of the µISP. That'll raise the price of it by a dollar, but that won't go into effect until the current inventory of 0.4 boards is cleared out.