Hi Wojtek,
Thanks for posting!
Yes - stack overflows are tough to deal with. I have a plan that should allow NCrunch to tackle this tidily, though it will take a bit of work and fortunately these issues are relatively rare in a developer's workday (unless your writing some manically recursive code). You'll notice that when these happen, the engine should just throw up and error and then carry on as usual.
Cheers,
Remco