One of my three successfully clear cup cuttings has a strong root that has just started growing upwards, all the way from the bottom of the cutting, and is growing up out of the soil. Should I let it do its thing or try to force it to grow back downwards?

Lots of mine do that.  I let them be, and they eventually dry out.  Doesn't affect the health of the plant from what I've seen.

It's very common for the roots to do that. I do the same as Frank and just let them be. They'll either turn and grow down or just dry up.

Just let nature take it's course...your trees will be fine...best if luck with all your fig projects.