Most of the games that have been deindexed on itch.io and some of the ones that were banned/removed were free or Pay-What-You-Want/Donation-Ware (some even via Patreon or SubscribeStar rather than itch.io's own payment processing).

The problem isn't just "the Payment Processor doesn't want to support this game" but also "this game shows Guilt-By-Association that your platform's money might go to 'criminals' or 'sinners'."

Guilt-By-Association is real gross, but a large part of the current fight, too, especially looking at itch.io's payment processor-required actions, not just Steam's.