Let's check the tape (recording):
“If she gets to pick her judges, nothing you can do, folks,” Mr. Trump said, as the crowd began to boo. He quickly added: “Although the Second Amendment people — maybe there is, I don’t know.”
His comment assumes she's already elected, that's why 'nothing you can do' hence the argument that he was only referring to not voting for her is rather weak. His own campaign referred to the comment as ambiguous, which it certainly was.

Hillary Clinton has not made any comment about changing the Second Amendment. Indeed, the Supreme Court cannot change the Second Amendment.  The Supreme Court may be able to affect the interpretation of the Second Amendment, which is not the same thing.

Donald J. Trump was certainly trying to exaggerate the fears of his followers and he made a provocative comment that many people, including me, thought crossed a line of appropriateness. I would feel the same way if Bernie or Hillary said it.