Sentence structure is totally independent of its meaning, or the thing it wants to convey. Your confusion greatly roots on the fact that you are so concerned on the actual meaning of the sentence rather than the structure itself.
But let me demonstrate why "because" falls into subordinating conjunction category:
In your example
He passed because he was intelligent.
Note that there is only one line of thought here: The mere fact that he was intelligent made him pass the exam. In other words, you are basically saying that being intelligent is a cause for him passing the test.
On the other hand
He was intelligent therefore he passed the exam
Note that there are two separate states here: first, the fact that he was intelligent; and second, the fact that he passed the exam. What "therefore" did is to combine these two separate facts in order to make an inference.
In grammatical theory, for theories based on hierarchical tree structure, No, because presumably grammatical functions correspond to the descending lines of a tree diagram, and no two lines can converge, allowing a single item to be the daughter of two different mothers. I know of two theories which do not require strictly hierarchical trees and which do allow a single item to have two different functions.
One is Relational Grammar (and Arc Pair Grammar), proposed by Paul Postal, David Perlmutter, and others. However, although it is proposed in this theory that some tree branches converge, I don't know that evidence has been given that this is actually so.
The other is McCawley's variety of transformational grammar, described in his textbook The Syntactic Phenomena of English, which includes an explicit account of a modified phrase structure theory that sanctions converging (and crossing) tree branches. Specifically, McCawley proposes that the raised node of right-node-raising (RNR) constructions simultaneously has grammatical functions in both of the conjuncts to its left. So, for instance, in
John built, and I installed the stove of, the new kitchen.
the raised constituent "the new kitchen" is simultaneously the direct object of "built" and object of the preposition "of".
McCawley does give some evidence for his theory of RNR constructions that is based on how the CNPC constraint works in some rather complicated examples, which I cannot recall in detail.
Best Answer
I'm not sure what is being asked here. Must the word "which" be by itself the whole subject? And must the same sentence be using "which" for both the subject of its main clause and for a dependent clause?
Anyway, this might help: a main interrogative clause using the word "which" as its subject,
though, those examples do not have a dependent clause in them.
Perhaps a supplementary clause could be added,
If the comma in that last example was deleted then that would change the supplementary clause into an integrated clause. That would give us,
That interrogative clause, with the integrated relative clause, seems to be using a "which" as subject of a main clause and also a "which" as subject of a dependent clause.
If a declarative clause is expected as an answer, then that might be a bit harder. Maybe a supplementary clause as a separate sentence might be acceptable?
For instance, using an example out of the textbook by Huddleston and Pullum et al., A Student's Introduction to English Grammar (2005), page 189,
(Note that "A" and "B" are two different speakers.) Using their example, perhaps consider the sentence,
or
And if the comma in that last example was deleted, that would give us,
That declarative clause seems to be using a "which" as subject of its main clause, and also a "which" as subject of a dependent clause.
If you are using a traditional grammar or a modern grammar that wouldn't accept that last example, because it wouldn't consider that relative clause to be "restrictive" in function, then perhaps consider,
.
These are just some thoughts. Hopefully they will provide some useful info for you.