"Even if every Chasidic voter in Borough Park voted for President Trump in 2020, he'd still stand no chance of winning New York state, the city, or even Brooklyn."

That set off a series of protests first from Rubashkin's own Chasidic community and then from a series of Democrat and Republican elected leaders who noted he was getting a more severe punishment than Enron's Jeff Skilling.

It was that bipartisan push for leniency for Rubashkin that the White House used as an explanation for the president's decision.

But clemency is usually not about bipartisanship; it's about rewarding or possibly gaining a valuable base of voters.

On an incredibly micro level, one could argue that President Trump was indeed playing to some of his base supporters with this move. While 71% of the Jewish community voted for Hillary Clinton in 2016, Trump won the American Orthodox Jewish vote and 68 percent of the vote in the heavily Chasidic and ultra-orthodox Jewish Brooklyn neighborhood of Borough Park.

But even if every Chasidic voter in Borough Park and Crown Heights voted for President Trump in 2020, he'd still stand no chance of winning New York state, the city, or even Brooklyn. Jews make only about three percent of the total vote in the U.S. anyway.

Another explanation for this decision could be campaign donations. That was the charge when President Bill Clinton pardoned financier Mark Rich in 2000. That move prompted an FBI probe in part because Rich's wife Denise had been making campaign donations to the Democrats.

The Rubashkin family has made donations to the Republicans in the past, but not to President Trump. The family is no longer very wealthy at this time. And while the Chabad Lubavitch network is a nonprofit powerhouse with worldwide reach and visibility, it doesn't make campaign donations or make official endorsements. So this decision to please the tiny Orthodox Jewish community still doesn't really add up based on the usual metrics.

But it starts to make sense in the context of another decision President Trump made recently that cheered that same religious community. That would be President Trump's move to change U.S. policy and officially recognize Jerusalem as the capital of Israel.

A major result of that decision is that it threw much of establishment Washington for a loop. It forced it to reconsider a key cautionary restriction the U.S. has always put into its otherwise warm relationship with Israel. In that way, the Jerusalem decision was about sending a message to the State Department's career bureaucrats just as much as it was a message to foreign countries.

Similarly, Jewish Americans have long enjoyed success and acceptance in the United States, but the Orthodox community has felt slighted by the justice system in some cases. That would include the Rubashkin sentence and the long sentence for the now-released Israeli spy Jonathan Pollard.

President Trump now seems to be sending a message about those sentencing and prosecutorial practices to the many Justice Department officials who were involved with this case and also to Judge Reade. No, the Rubashkin commutation didn't gain the kind of headlines the Jerusalem decision did. But career federal prosecutors are not likely to miss this news.

President Obama did something very similar at the end of his term, albeit on a much grander scale. He decided to grant hundreds of commutations and pardons to people convicted of drug-related crimes. That move was meant to send a much larger message about our drug laws and sentencing rules.

The difference in the timing stands out. Most presidents wait until their final days in power or at least their second terms in office to grant clemency in order to avoid any political backlash. Love or hate President Trump's decision to pardon former Sheriff Joe Arpaio and give Rubashkin this commutation, at least he's had the guts to make those moves at a time when it could actually cost him.

The final cost/benefit analysis makes it clear that this was not some kind of Trump reach for an all-too-small Jewish vote. This makes much more sense as the way to send a message to the establishment, or "the swamp." Whether the swamp gets the message and responds accordingly is yet to be seen.

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

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