Meh, putting the blame on third-party candidates or their voters is obviously wrong, but it's undeniable that if a voter genuinely cares about preventing the worst outcome, then the only worthwhile course of action is choosing the lesser evil.
But lesser of two evils is still bad, because the consequence is always evil.
You say the crazy scenario that if all the Clinton > Trump voters vote for another option but all the Trump > Clinton voters vote for Trump, Trump will win, but what about the not any crazier scenario where a vast majority of voters from either camp vote for their actual favorite, regardless of party affiliation? The consequence of that is a functioning representative republic, freed from the two-party system of evil vs. evil.
The Democratic and Republican Parties are designed to appeal to a broad group of people. Even if people voted on a "What's your favorite party?" election with no consequences whatsoever, the Democrats and Republicans would come out on top. Just because you would prefer Johnson doesn't mean most people would. Personally, I see Clinton as the least of four evils, not the lesser of two, and I think many Clinton supporters would agree with me on that.
Also, I can't actually control what Trump>Clinton people do, so I'm going to use my vote to counteract theirs. Voting Stein on the assumption that some conservative is going to vote Johnson or whatever is a terrible idea.