It would appear that this is an XY problem, where Y is what you’re asking ( an attempt to solve X, your real problem ), and X is the inability to retrieve only confirmed/active users
Firstly, what you wanted to do isn’t quite possible in multisites, there’s already a table named wp_signups for these users, that tracks the pending confirmation and necessary keys, since a user might be confirmed on one blog and not another. So deleting users that aren’t confirmed for your root blog, might delete users that are confirmed on other blogs, destroying data/logins.
So I’m going to answer your original problem, in the context of a singular site, as it’s significantly simpler:
SELECT * FROM $wpdb->users WHERE user_status != 2
Taken from the plugin named unconfirmed, but with the logic flipped
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