Zooney,
My solution is to add the filter I mentioned in my original post:
add_filter( 'shibboleth_user_nicename', 'sanitize_title');
You can either create a single plugin with this line, or, to keep it simple, you can just add it in the shibboleth.php code.
I’ve added mine just above
$shib_headers = shibboleth_get_option('shibboleth_headers');
inside the shibboleth_update_user_data function.
Hopefully this can be integrated into future releases.