When Bernard brings Linda and John back to the World State, describe the director's reaction.

Bernard laughs and introduces Linda. Linda quickly recognizes the Director, calls him by his name, Tomakin, and rushes up to give him a hug. When he pulls away out of disgust, Linda angrily screams at him for leaving her on the Reservation while pregnant with John. The Director becomes even more mortified when John walks in, falls to his knees, and calls him "father," a word filled with embarrassing meaning. All the workers begin laughing until the Director finally runs out of the room.

Did Thomas go on a PERMANENT soma holiday after this?

The Director decides to resign his position because the shame of being a "father" is too great. I don't recall if he went on a permanent Soma vacation or not.