Let's put it this way. Without his supporters, the Republican party can't win the general election. So either the Republican party accepts them if they want to ever beat the Democrat party again, or they reject them, and they might end up forming a strong 3rd party later on, and help change the laws so they are more fair towards 3rd parties.
He has not shaken up the GOP whatsoever. He has arguably shaken up the Libertarian party, but his base has nothing in common with the GOP base.