John Calvin Commentary Numbers 16:21

"Separate yourselves from among this congregation, that I may consume them in a moment." — Numbers 16:21 (ASV)

Separate yourselves from among this congregation. Again God declares that He will no longer bear the people’s great impiety, but will destroy every one of them. Therefore, just as He had commanded Lot to depart from Sodom, even drawing him out by the hand of the angel when He intended to destroy that city, so He now commands Moses and Aaron to give Him space to exercise His wrath.

In this, He declares His extraordinary favor towards them, as if He were not free to execute vengeance until they had moved out of the way, so that the destruction would not reach them. However, in speaking this way, He does not absolutely affirm what He had determined in His secret counsel, but only pronounces what the authors of this wickedness deserved. It is, therefore, just as if He were ascending His judgment seat.

Thus, Moses, by his intercession, by no means changed God’s eternal decree; but, by appeasing Him, delivered the people from the punishment they deserved. In the same sense, God is said to be influenced by our prayers; not that He assumes new feelings in the way humans do, but, to show the more-than-paternal love with which He honors us, He, as it were, indulges us when He listens to our desires.

From this we gather that even by this express denunciation, Moses was not prohibited from praying, because his faith in the adoption of the people was not destroyed. For we have already said that this principle—that the covenant God had made with Abraham could not be nullified—was so thoroughly engraved on his mind that it surmounted whatever obstacles might present themselves. Resting, therefore, on the gratuitous promise, which did not depend on men, his prayer was the offspring of faith.

For the saints do not always reason with accuracy and subtlety about the form of their prayers. But after they have once embraced what is sufficient to awaken confidence in prayer in them—namely, God’s word—their whole attention is so directed to it that they overlook things that seem to contradict it. Nor can we doubt that it was God’s design, when He delivered His terrible sentence concerning the destruction of the people, to intensify Moses’ earnestness in prayer, since necessity increasingly inflames the zeal of the pious.

In short, Moses was always consistent in his care for the well-being of the people.