Maybe it's a bit naive, but isn't that what federation is supposed to solve? People who are more security-paranoid can forbid clients which don't have the highest security certification, and operators who aren't so diligent will be fine with signed clients being run on untrusted hardware.
I mean... is there any open-source software being developed today which enforces key security in secure hardware enclaves? Verifying the GPG signatures on binary packages is "good-enough" for most operators. Build reproduceability will help to further reduce trust of unverified hardware.
It seems to me the job of the protocol, and baseline/recommended UI/UX, is merely to help users make informed decisions. Security is a spectrum, and if signed clients improve security (while not fraudulently representing itself as perfect or near-perfect security, if it were running on trusted hardware), then that's a net benefit to the open network.
This certainly needs more thought :)
It's possible that just relying on social mechanisms may be enough to discourage people from running known evil apps (similar to educating users not to install malware today, or do trusted operations with cybercafe computers, or whatever). Effectively, the verification process when going and explicitly trusting a new device needs to explicitly prompt the user to consider where on earth this app came from, and if it should be trusted.
The only alternative is really DRM, which just feels wrong.