The clearing house doesn't know who is trading on margin and who isn't. They don't have visibility into the brokerage's interactions with their clients. They can't "only allow trading for non-margin accounts".
To be clear, the RH T&C very broadly protect them in case of any arbitrary service interruption, so on paper they're probably entitled to do whatever they want. But at the end of the day, it was them who got caught with their pants down because they went too far in their UX/risk tradeoff, and now users are paying the price and are understandably pissed.