"[I]f President Trump is only going to make piecemeal changes to the federal bureaucracy based on personal issues alone, his supporters are going to get discouraged rather quickly."

And perhaps he'd still be there had Obamacare not gotten in the way. Remember that President Trump on his first day in office signed an executive order allowing federal agencies to waive enforcement of certain aspects of Obamacare. He further boasted on Oct. 16 that his more recent executive order suspending federal subsidy payments to Obamacare insurers meant there was "no such thing as Obamacare anymore."

And then four days later the IRS came in to spoil that party by issuing a statement saying it would not accept any tax returns that did not include the filer's health-insurance status. Just like that, the most crucial part of Obamacare, the individual coverage mandate, was still very much alive.

That was clearly the final straw. The fact that the Trump team made this move just a week after the news broke about the IRS Obamacare defiance is hard to ignore.

It's also hard to ignore that this news comes on the day after that the Trump administration settled lawsuits with dozens of tea party groups who sued the Obama administration over the IRS anti-conservative targeting scandal.

So the swamp perhaps is effectively drained at the IRS, but it sure looks like it took a brand new case of personal defiance against this president and his administration to make it happen when it did.

This is no way to fix Washington. And it's not the first time this has happened.

President Trump could probably have done much better with a sweeping set of dismissals on day one, including then-FBI Director James Comey. A consummate outsider like Trump would have had plenty of political capital to do it. But instead, he's chosen to either not make the changes at all or waited for personal slights to get moving. In Comey's case, even the conservative National Review's sources say the decision to oust him came only because President Trump was angry that Comey made it sound like he was personally under investigation.

So, where does that leave us? Will most career bureaucrats in the federal government remain safe in their jobs unless they commit similar public acts of defiance against the president himself?

That would be too bad. Because distrust and dislike for the entrenched political establishment from both parties is actually on the rise and one of the unifying factors still viable in America. People like Donald Trump don't get elected and back-benchers like Senator Bernie Sanders don't nearly take a major party nomination if that distrust and anger isn't real. And since no one is really calling for a French Revolution-style violent overthrow of that establishment, President Trump can achieve a happy medium for almost everyone simply by firing Washington careerists who will likely find safe landings in the private sector.

But the time is running out for that kind of peaceful housecleaning, especially if President Trump never really intended to do it in the first place. And lest anyone think that ignoring the base that turned the tide in this past election is wise, take a good look at the fates of Senators Jeff Flake and Bob Corker.

"Draining the swamp," as distasteful a term and goal as many Trump opponents believe it is, is still one of the key rallying cries for that base. But if President Trump is only going to make piecemeal changes to the federal bureaucracy based on personal issues alone, his supporters are going to get discouraged rather quickly.

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

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