The simplest fix would be: "Freedom is for THEY who UNDERSTAND their rights along with THEIR duties". The word following "for" should be in accusative case. You don't need the "as well", because you've already said that with "along with".
You could also use THOSE instead of THEY. That would make it plural, but I think think the
>Freedom is for THEY who UNDERSTAND their rights along with THEIR duties
Sorry, but I don't understand why it should be THEY, not THEM. With my limited grammar knowledge, I think "who UNDERSTAND their rights along with THEIR duties" is a relative clause. The sentence will still be grammatically correct if the relative clause is omitted. If so, it becomes