The MTA can fire them - It's perfectly legal to do so, under the Taylor law. The MTA board members are appointed by Pataki, Bloomberg and suburban county executives. Pataki really controls it at the end of the day. Bloomberg has some say.
Nobody will be fired. It's impractical - how many people do you know that how to drive a subway? And so far, most New Yorkers support the union (52%-40%), according to
Survey USA, believe it or not. Unfortunately, this is the reality of living in liberalland - there are many, many pro-union liberals here.