Application that processes XML based on configuration
Pardon my lack of Python knowledge, but I think a function something like this might work:

def fatal_error(message):
    log.error(message)
    app_exit(1)


And now your catch cases look more like this:

try:
    root = get_root(xmlfile)
except ET.ParseError as e:
    fatal_error("Error while parsing {0}: {1}".format(xmlfile, e))
except IOError as e:
    fatal_error("I/O error({0}): {1}".format(e.errno, e.strerror))

log.info('Getting configuration of XML {}.'.format(xmlfile))
try:
    cfg = get_cfg(xmlfile)
except IOError as e:
    fatal_error("I/O error({0}): {1}".format(e.errno, e.strerror))