Jumping off of this question, I'd like to know how to gracefully detect and remove each snippet in the WHERE clause of my query object in plain old hook_query_alter(), not hook_views_query_alter() (as the Views query object seems structured in some entirely different way (frustrating!). The documentation vaguely suggests that this is possible by showing how you can create a reference to your query conditions that you can then manipulate, by starting with this:
$where =& $query->conditions();
... but the object(s) within are utterly confusing, and I've been struggling to remove or replace existing snippets. I've explored /includes/select.inc and /includes/query.inc but the classes therein don't seem to provide any methods for fine-tune manipulation.