On the issue of subsequent invalidation of all submitted certificates, this is prevented by submitting to at least 3 different entities (as of now, there's a discussion whether if this should be increased), so if a log is subsequently found to be corrupted, the operator can send a "operator error" signal to the browser, and any tampered logs are blacklisted from browsers. (Note that all operators of CT lists are members of CA/B forum, at least as of 2020. In standardisation phase, some individuals have operated their own servers but this is no longer true.)
* Note that if the cert details are nonsensical but technically valid, it is still accepted by design, because all pre-certificates are countersigned by the intermediate signer (which the CT log operator checks from known roots). If the intermediate is compromised, then the correct response is obviously a revocation and possibly distrust.
° At least the human-induced variety, you could say that this incident is technically a software bug that occurred due to a hardware fault.
If Yeti can't handle corrupt data and falls down like this, Yeti seems pretty broken to me.
The protocol here seems to have done what it was designed to do. The corrupted shard has simply been removed from service, and would be replaced if there was any need. The ecosystem of CT logs foresaw this and designed for it.
You can argue if the software running the log should have verified that it calculated the correct thing before publishing it, but that's not a protocol concern.
Really the bigger news here seems to be a software bug: the CT protocol wasn't tolerant of bad input data and was trusting actors that clearly can't be trusted fully. Here the "black hat" was a hardware glitch, but it's not hard to imagine a more nefarious trick.