The way for President Trump to handle the newly energized collusion investigation by is massive retaliation...
1. Trump should advocate in public, and then if necessary assert through his authority, that the investigation of the election by Mueller is to be expanded to include all participants and all activities in the campaign without limit.
Mueller's new charge would be "to determine whether there were any irregularities of any nature whatsoever in the 2016 campaign from any source whatsoever," with a special focus and separate report on the violence at Trump rallies. This separate report will include a description of the participants in the violence; their method of organization and transportation; their leadership – including the roles of Robert Creamer and Scott Foval, if any – and how, by how much, and from whom they were financed.
The point is that Trump doesn't fire Mueller, but rather, in the interest of justice, expands his remit.
2. Then the second thing Trump does is to get a special counsel appointed to investigate whether the use by Hillary Clinton as secretary of state of unsecured communications did any damage to the national security and national interests of the United States in any way whatsoever and to prosecute any violations of the law found in the course of that investigation, including any irregularities in past investigations.