Working off of Pieter Goosen’s answer to this question, the way around this is to create a list of all the categories except the one you want to exclude, then search for posts that include them. That way, if a post has the excluded category but also other categories, it’ll be included. So, in my case:
$args = array ('exclude'=>1,'fields'=>'ids');
$exclude_uncategorized = get_terms('category',$args);
and then include the following in the $args for the wp_query:
'category__in' => $exclude_uncategorized,
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