"The good news is that none of this should disqualify any of the evidence Mueller and his team have uncovered so far. If there is something leading to a possible smoking gun in the case, Mueller's removal in no way erases that evidence."

Either Mueller knew about that controversial move and hired Strzok anyway, or he was unaware of it. Either are unacceptable mistakes. Mueller must take full responsibility for the error by stepping aside.

Strzok is the worst example, but there are other questionable staffing decisions. The Wall Street Journal reported that Mueller investigator Andrew Weissmann attended Clinton's election night party. In January, Weissmann also reportedly praised outgoing acting Attorney General Sally Yates, after she was fired for refusing to defend President Trump's travel ban.

Investigator and attorney Aaron Zebley once represented Justin Cooper, who was responsible for helping set up the now-infamous Clinton private email server. Cooper later admitted to helping to destroy Clinton's old mobile devices.

In fact, a total of six of the 15 lawyers on Mueller's staff have been connected to either the Clinton campaign or actions that can be viewed as overtly partisan.

The other big problem is the constant leaks about details of the investigation. While it's not realistic to believe a crucial investigation of a sitting president can maintain an airtight level of silence, the regularity of these leaks is troubling. For those Democrat-leaning members of Mueller's team, it must be very tempting to use leaked details and partial information to poison the public against President Trump and his family.

Mueller has either been unwilling or unable to plug the leaks, yet more evidence that he should step down.

The good news is that none of this should disqualify any of the evidence Mueller and his team have uncovered so far. If there is something leading to a possible smoking gun in the case, Mueller's removal in no way erases that evidence.

If the compromised Mueller stays on, however, a significant segment of the population on either side will reject his findings. If the evidence incriminates President Trump, Trump supporters will be much less likely to accept it. If the findings exonerate the president, Trump opponents are more likely to believe the partisan pressure on Mueller led to a whitewash.

The worst case scenario is that the criticisms against Mueller push President Trump into firing him. That bad decision would set off a true constitutional crisis and would almost surely lead to massive and crippling protests.

The better scenario is for Mueller to step down voluntarily. Let's face it, trust in government and even government law enforcement is at a low ebb right now. The Clinton email scandal, the IRS targeting scandal, and now questions about the integrity of this Russia probe have taken a serious toll.

Mueller can go a long way to restoring honor and trust by stepping aside in the name of avoiding the appearance of impropriety. This would stand in great contrast to government officials from both sides who now routinely deny they should be held to the same standards as the rest of us.

The longer Mueller sticks around, the more time critics will have to undermine the probe by attacking him and his senior team. For those on either side who want to see a solid conclusion reached in this case, it is obvious that Mueller must sacrifice himself for the greater good.

Commentary by Jake Novak, CNBC.com senior columnist. Follow him on Twitter @jakejakeny.

For more insight from CNBC contributors, follow @CNBCopinion on Twitter.