Macro Videography: Lenses, Camera Options
You are absolutely correct that a good macro lens is crucial for a specialty such as shooting miniatures.  You are also correct that cropping into a 4K source to get an HD frame will still give you good video quality.  And it's also true that a RAW image format like BMCC is somewhat forgiving of not only cropping in, but zooming in to some extent.  But I would also caution that once you actually start zooming into consumer-grade digital video, it falls apart way, way faster than when you zoom into typical stills photos.  Since the SONY cannot record 4K natively, but only with an expensive external recorder, and you've set a budget ceiling of $2K, that means no zooming with the SONY.

I have three Canon macro lenses that are each great at what they do: the 100mm f2.8L, which is the simplest to use, the 180mm f3.5L, which is better for shooting nature (more working distance), and the 65mm f2.8 Macro Explorer, which shoots between 1:1 and 5:1 magnifications (great for bugs and other tiny, tiny details).  I don't use my Canon lenses on my GH4 (I also have a RED WEAPON with a Canon mount), but to answer your question, I'd pick the 100mm macro with a speed booster (not for f2.0 performance, but for field of view) and a GH4.  And I'd make great use of my K*FLect light reflector system to light my tabletop scenes.