You could install OpenSCAD on the Jobe server and write a Python-based question type that submits students code to be run by SCAD. The problem comes in grading the result, probably (as you suggest) by analysing an export file such as STL. That's a hard problem in general, though you might be able to do some useful checks using the built-in Regular Expression grader. My gut feeling is that it's not worth pursuing unless you have large classes (I'm talking hundreds of students) or if someone else has done all the hard work for you already :)
I like teaching my students to create 3D models using OpenSCAD. It's a great review of geometry and is also a great way to review programming concepts in a different context. How hard would it be to make CodeRunner work with OpenSCAD? I imagine it would be a matter of comparing STL files? I'm guessing this would be a major project, but figured it's worth asking on the off chance it's doable without too much effort.