Remember when conservatives were upset about the (mostly overhyped) claim that Barack Obama had politicized the IRS to target conservative groups (despite the fact that Obama himself wasn't involved, and liberal groups were also targeted, and the IRS admitted the mistake when it came to light and changed policy). Trump's longing to control the FBI and the Justice Department and military justice is exactly what conservatives accused Obama of, except that these organizations have even more power to ruin people's lives. Executive agencies should not be politicized in this way, because it is authoritarian and dangerous to a free society.
If Trump keeps jumping the gun on the justice system, he's going to undermine and destroy quite a number of prosecutions. And it is, all by itself, an impeachable offense, should Congress ever take an interest in the rule of law again.