Do you know of any non-Eagle tools for calculating the "isolation milling" G-Code required from a Gerber?
I thought I had seen some, but they're not showing up when I look for them 
LPKF's "CircuitCam" will output HPGL paths for isolation, with billions of options, but it's commercial software and expensive... (It's intended for use with their own CNC PCB routers, of course. But the HPGL output might make it generally useful...)