This sentence is strange in English. Does "třída" mean both "grade" and "classroom" or "class"? Does the sentence mean "what grade is she in?"
"Třída" really does mean both "classroom" and "grade".
However, as you say, this Czech sentence is talking about grade in which she is in.
"To which grade does Zofie go?" is also a correct alternative.
What grade is Zofie in? Would normally be used. Literal translations often don't work very well.
"What grade is Zofie in?" is also accepted.
I would recommend this as the default translation. You and I come from the same region in the US -- have you ever heard or read the 'go to' version?
I have not heard the "go to" version, but it does reflect the verb used in the Czech original. However, we have changed the main translation to "What grade is Žofie in?" in accordance with common AmE usage. I don't know how quickly it will update.