The creation of a "permissioned asset" is possible due to the "universe" function (as written before, an universe in Taproot Assets is sort of an "official block explorer", but it's not necessarily centralized on a single server). See a description of universes here. This indeed gives the issuers (in this case: Tether) some control: they can create custom rules for the assets which will be included in this universe. It's likely that Tether will designate their own universe as "default" for USDT.
Lightning Labs also creates and manages universes, and thus it's also possible that Tether and Lightning Labs agree that LL always will use Tether's universe as well, although this for sure would be seen as controversial and a step towards centralization. It is however also simply possible that LL agrees to abstain from creating an own universe for USDT, so Tether's universe becomes the only "official-looking" one.
So if an USDT transaction X is marked as "disavowed" by Tether (e.g. as the result of a hack, or sanctions evading etc.), I imagine they can create a rule in the vein of "has no antecessor:X" for the universe, and thus the subsequent transactions won't be displayed on this "official block explorer" of the universe. Everybody who's aware of the universe (including wallet software) would thus not "recognize" these transactions as valid.
Those owning the "disavowed" tokens would likely try to create an own universe where the transactions are still valid (like Pmalek wrote here), and lure other users into buying or accepting these tokens by using other "alternative" universes for the USDT token. But that won't be easy, I think.