What's wrong with making 3 or 4 in-camera negatives? SOme photographers were still shooting separations in the 70's and early 80's, and that's all they did before that (for the really good work).

I've never worked in color separations, but all it is is making three or four identical negs but with different filters. Granted, with subjects which aren't totally stationary it might be a bit of a problem (unless you want to build a custom camera) but it's doable.

Oh, also, I guess this is what should come to mind first, since it was the method used up until (relatively) recently when the press world went digital:
You shoot regular color film and then, in the darkroom, make (contact or enlarged) separations from the original neg.