fixed runscript to handle SystemExit

The function 'popenscript' in test_scripts.py failed in my dev environment, because I am not running the tests after installing khmer in a virtualenv, and so khmer could not be imported.

Upon further investigation, this function existed solely to deal with argparse option testing.  This was necessary because the runscript function didn't handle SystemExit properly.  I fixed that, cleaned up some related code, and removed the now-unnecessary popenscript function.

Along the way I also fixed some incorrect status code checks that were only succeeding because SystemExit wasn't handled properly.