Agreed about waterjet leaving frayed edges, I had the same result. It causes the composites to de-laminate, but I will say that the waterjet cut will be pretty consistent, which might be workable for you.
Milling it is not difficult, but the results will vary wildly depending on how you hold it down. Myself I don't accept most carbon fiber milling work if there's any sort of accuracy requirement for it, since the material can be difficult to control. I'm probably just too picky, but usually the remaining jobs are just trimming panels that are made for other parts where they don't really need to be any size in particular, just "trimmed".
You run into similar issues that are encountered with other "sheet" material, like the sheets rattling and being pulled up, chips getting down beneath it, areas vibrating like crazy, etc. Most of the composite-specific high-end cutters are reverse-fluted such that they apply force downward against the workpiece, rather than a typical endmill helix which sucks the part up. That type of thing can help but it's only if you want to buy a bunch of brand new cutters from high-dollar companies, which probably wouldn't be too cost effective.
I've had only limited success laser cutting the stuff, since it requires a lot of power and must be run slowly. We use a 200 watt CO2 laser for it. The problem is, the fibers require much higher power to cut compared to the composite resin, so it's not pretty and the edge can be very sharp which almost always necessitates sanding or otherwise blunting the cut afterward. Waterjet has the advantage there, but hey it's waterjet....
If it's a fabric sheet that has yet to receive the resin, the situation is much improved, but that's a whole difficult application.