There’s a good HN thread from earlier this year about that, but basically, you can disable iCloud Backup and enable Messages in the Cloud, so that all of the messages are still backed up and synced between your devices but the keys are not, so that Apple can not read them. Then you can back up to your Mac/PC instead.
But most end-to-end encrypted apps aren't configured by most of their users to send their messages and encryption keys directly to the author of the app. iMessage is.
