Is it OK to run 12-3 cable to a ceiling fan from a switch that's wired with 12-2?
Either is fine.

I'm a little concerned with what you mean for the the "crimp" grounds in both cases. So long as it's an approved connection method, fine (I finally gave up and bought the overpriced green wirenuts.)

Given that you want separate switching, and have the wire to support it, separate switching would be preferable.

You also need to be sure that the switch box is large enough.

1 ground (they only count once) 2 yokes (unless you use a 1-yoke double switch) at 2 each, 2 wires in, 3 wires out (clamp in box or exterior?)

1+2+2+2+3 = 10x 2.25 (12 Ga) = 22.5 cubic inches (or 24.75 with clamps in the box) for the two switches on 2 yokes configuration. Larger is fine.