I think Trump sought the Presidency because of what you have just said. He recognized the problem, believed that he could correct it, and has, so far, succeeded. I'm convinced that his motives are benevolent and his standards the highest.
I hope that the Justice Department, in the Trump Administration, will be unfettered, uncorrupted, and free of political influence. If so, the question of the prosecution of the Clintons will be decided on the merits of the case, which, of course, is as it should be.
Trump might have to be reminded that NO ONE is "too big to prosecute" and that to refuse to prosecute someone because of high position is as unjust as to prosecute someone because of high position and either case would violate the equal protection clause of the Constitution.
Trump has vowed to "clean up Washington", i.e. to end the corruption. Nothing is more corrupt than the Obama Administration and the Clinton Enterprise. Trump must NOT refuse to investigate, prosecute, and do whatever is necessary to clean up the corruption, regardless of the consequences, and certainly not to avoid a Constitutional Crisis. As you say, we have been in a Constitutional Crisis for 8 years--maybe longer (e.g. George W. Bush refused to enforce US immigration law despite his responsibility and Oath of Office to do so).
Ah, we have an accord! ;-D