You're correct that Trump did not use the words "someone should kill Sen. Clinton." What he did was imply that the Second Amendment fanatics might be able to prevent Hillary Clinton from picking judges when she becomes president, the implication being that extralegal measures would be used since that's what distinguishes the Second Amendment fanatics from regular citizens. The guns and what Trump implied was the willingness of Second Amendment fanatics to use them could perhaps, according to Trump, prevent Clinton from appointing judges as she sees fit as the duly elected POTUS. Here's what he said:
"Hillary wants to abolish, essentially abolish, the Second Amendment, by the way, and if she gets to pick, if she gets to pick her judges, nothing you can do folks, although the Second Amendment people maybe there is, I don’t know but, that will be a horrible day, if Hillary gets to put her judges…”