In my opinion this isn't really a big concern. You could read the Database directly anyway, so it would only prevent people that don't know what they are doing (and if they don't know what they are doing there is a good chance they couldn't setup the instance in the first place). Besides that you need to trust your instance owner anyway to keep your stuff safe. The only other option is to wait for E2EE for DMs at which point the instance owner can't see anything.
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Comment by @SteveLinkNoah