"Root of trust" are wrong words.
Anyway, if the adversary was issuing conflicting milestones (by confirming transactions leading to an inconsistent state of the ledger) then IRI would stop updating confirmation status of the transactions. That would require human intervention to resolve which might look as node operators approaching the original coordinator operator and asking for a new public key derived from a new private key.
It should be emphasized that the full nodes don't trust the coordinator's milestones, the nodes use the coordinator for finalization of the transaction status, not for deciding if a particular transaction is legitimate or not.