Please excuse my total ignorance of SCPI, so I may have this wrong.
It looks like a pretty simple task to make a USB dongle to enter the code a boot.
ie wait 15 sec after powerup for boot to complete send SCPI string - gross over simplification but you get the idea.
I have Tweeny 2.0 sitting here just waiting to do something really useful
http://www.pjrc.com/store/teensy.html
Actually it's not that much of an over-simplification at all. I've been using a RPi to control my DS2000 to have a set of extra hot buttons. I wrote all the comms stuff for it using pyUSB and the USBTMC class is actually very simple to implement. However I've been using a RPi because I wanted a button to that when pushed, it would dump a BMP to a network drive and record audio from a USB mic until the button was released, and store the MP3 with the BMP. As a single button record capture if you will.
But it would be basic to port what I've done across to something like the Microchip USB framework, then any PIC with a USB OTG port could do this. I don't have any experience with the Atmel USB framework, so it's unlikely that I'd port it across to that (and I don't have any usb OTG AVRs.)
Tell you what, I'll add it into my RPi code and post this afternoon. There's probably way too many RPi's sitting around doing nothing at the moment anyway.