No. They blacklisted the stolen tethers, and all they now have to do is issue a new batch of $30 million worth of tethers. In no way this puts them in the red.
It seems like people did in fact notice the $30m being deposited on Bitfinex and being used to buy Bitcoin, all before it was known to be stolen. Difficult to confirm a thing like this, but I wouldn't bet against it.
But since Tether Limited are the ones who back the tokens with real dollars, they can effectively unilaterally pressure anyone to upgrade the client. Those who don't upgrade and accept stolen tethers will be left with worthless unredeemable tokens.
Read this lawsuit: Tether only has $50 mill and their wires have been frozen by Wells Fargo since March 2017. So the remaining $600 mill tokens are backed by nothing.