Translation:I wanted to know who had helped the students.
What if there's just one student? In that case there would be no way to tell who's helping who, right?
Maybe passive voice would be more useful here?
"Ik wilde weten wie de leerlingen had geholpen," for "I want to know who had helped the students," and
"Ik wilde weten wie door de leerlingen was geholpen," for "I wanted to know whom had been helped by the students."
(I'm not completely sure that "door" is the correct preposition in the second sentence.)
(And as an aside, in English, in addition to our word order, "who" or "whom" should provide a sufficient clue for the difference in meanings, since it would be "who helps the students" or "whom the students help." But that assumes that people will remember to distinguish subjective from objective case in our pronouns, which sadly is a disappearing practice.)