The whole class fell silent or felt (shocked|surprised|sad) when they found out that Mr. Smith had passed.

Correct here would be 'fell silent'. 'fell' cannot be used with the other words. You could say 'felt surprised', but it's strange to talk about the emotions of a group of people that way, because how could the narrator know? For that reason 'fell silent' is the best choice.

Hey! I'm still alive! (Just joking, but it is weird to have a name that is so often used for hypothetical illustration.)

Yes, you can use any of those words to describe how a class might feel after learning someone passed away. However, you will need to change the wording a bit to fix the feeling you want to express. I would also suggest using the word "learned" instead of "knew", because it suggests the class is just now learning the horrible news that Mr. Smith passed away. For example: The whole class fell silent when they learned that Mr. Smith had passed away. The whole class was shocked when they learned that Mr. Smith had passed away. The whole class looked sad when they learned that Mr. Smith had passed away. You can also use more than one adjective to describe how the class reacted: The whole class looked sad and surprised when they learned that Mr. Smith had passed away. The whole class looked shocked and sad when they learned that Mr. Smith had passed away.