It seems to me that CT (or its operators?) should take a lesson from adversarial blockchains (cryptocurrency) here: a new state should not be propagated without verification.

I think that, for CT, this should be fairly straightforward. Some machine with access to the signing keys should generate new nodes and signatures and push those internally to some front-end machines. The latter (on separate physical machines) should fully validate the result before propagating it any farther. No outside user sees the result until at least, say, 3 machines fully validate it. Then, if validation fails, the state could be rolled back internally.

When a rollback occurs, the signing machine would think it’s signing a new, conflicting state, but that’s fine: no one outside the log operator has seen the old conflicting state.