Simply put; there is still a lot of legal issues surrounding Trump; from Trump U, to his connections with Russia. Any one of them can potentially put him in jail if any explosive evidence comes forward. If Trump is charged with a serious crime before the inauguration, the matter on whether we should disqualify the results should be taken to SCOTUS with the requirement of a unanimous decision from all justices. If all justices agree, then the runner up and their pick will be elected as President and Vice President.
Of course, this is just an idea and a policy idea that won't happen before the Inaguration, but Trump is an abnormal candidate, with abnormal circumstances. Who's to say that it won't happen again? That's why I think there should be an amendment that deals with this issue.