Good point about the graphite dust, maybe a vacuum cleaner would sort that? But you say "(+ laser)" so are you intending to cut graphite with a laser rather than an endmill? I imagine that in that case the material will just turn to CO2 which isn't great for the planet but the quantity will be small. Is there a danger that the graphite will actually catch fire?

For laser cutting I guess workholding is much easier since the side forces will be zero so should just need some location by double sided tape. Look up laser cutting graphite on Google, quite a few references though it looks like quite a powerful laser is needed.

For cutting simple rectangular shapes the g code is very simple even to write by hand. I'd be happy to write an example if it would help, assuming that you would be using a routing cutter rather than laser.