The destruction of Room Nineteen took exactly thirty-seven seconds. (11.12)
You remember Room Nineteen, don't you? You might have even giggled a little at the idea of unscrewing all the screws in the furniture, so it all falls apart at the slightest touch. But when we see The Goober trapped in the room, forced to sabotage the furniture against his will, this Vigils assignments is a bit less appealing.
There's something fascinating about the idea of all the furniture falling apart, the blackboard sliding down the wall, the general chaos. So, what's the big deal? Why does it hit The Goober and Brother Eugene so hard? Well, we don't see Brother Eugene's thoughts, but his tears speak volumes. We also don't know exactly what happens to him after his classroom is destroyed, but it's strongly suggested that he has "a nervous breakdown" (13.9).
The Goober tells Jerry that Brother Eugene took it so hard because, "Some people can't stand cruelty" (23.22). If The Goober is right, Brother Eugene is so devastated because it makes him think the students hate him so much, they want to tear up his class. Since he's a sensitive guy, this is a huge blow to his self-worth, as a teacher. It's no wonder he left the school, whether he has a nervous breakdown or not.
In any case, The Goober is suffering from guilt and from fear of being found out. He feels directly responsible, because he accepted the assignment. He also knows that if he'd refused, and if he refuses other assignments, it will result in personal pain. So, in addition to guilt, The Goober is suffering from a sense of powerlessness, and he's reminded of it every day. Room Nineteen, we are told, "would never be the same again. The furniture creaked weirdly, as if it would collapse again at any moment" (13.29). The room, then, becomes a micro-symbol of Trinity as a whole, a place so badly broken it will never recover.