Hi, thanks for posting.
Right now, there is no way to avoid cleaning up the workspaces at the end of the run with the console tool.
Since it's basically just a headless client, it has more or less the same bootstrap sequence and follows the same execution pattern (load, build workspaces, build projects, analyse them, run tests, clean everything up, terminate).
It would be advantageous for the console tool to preserve workspaces between sessions, or even to not use them at all, since concurrent changes to the foreground solution aren't usually a problem.
This is one of the things that has become more clear as we've continued to develop the tool: The original scope for the console tool was for a headless client, when actually it seems what was needed is a parallel test runner that can work inside a CI system. There's a whole lot of complexity inside the NCrunch engine that adds no real value to the console tool and generally just takes up time/CPU.
One of the problems we're facing at the moment is that the console tool was only really intended as a side feature, but it's become a bit of a monster on its own. We spent a considerable amount of time last year to bring it up to a more useful level. This is happening at the expense of the core product itself (which for the sake of revenue, is actually the important one). So in the near term, I don't see us doing much more on the console tool beyond basic operational fixes. The long term is less clear.
You're welcome to track this one on uservoice if you like so that it doesn't get lost. I don't think it's been requested yet.