Subscriptions should automatically be cancelled for channels that are no longer affiliated
Twitch should not renew subscriptions to channels that have left the affiliate program.
You can't subscribe to channels that are not affiliated, but Twitch will still charge you for the renewal if you were previously subscribed and that sub isn't manually cancelled. Since the streamer is no longer an affiliate, that presumably goes straight into Twitch's pocket as that channel does not have monetization enabled and cannot be paid out.
Refunding a subscription renewal is not technically allowed according to Twitch's refund policy, but their Support team can offer a "one-time" refund as a show of "goodwill" in these cases, even though the charge should not happen in the first place.