simpletest calls to url() causing PDOException errors

drupalGet() calls the url() function, which runs drupal_alter() on "url_outbound". This in turn runs hooks from other contributed module on the main actual site. In the context of, for instance, BasicUpgradePath, the tests are not running in an environment that can support those modules. So in this particular example, I end up with

PDOException: SQLSTATE[42S22]: Column not found: 1054 Unknown column 'source' in 'field list': SELECT DISTINCT SUBSTRING_INDEX(source, '/', 1) AS path FROM {url_alias}; Array ( ) in drupal_path_alias_whitelist_rebuild() (line 381 of /path/to/docroot/includes/path.inc).

because at that point in the test url_alias is the 6.x version.