Targum Pseudo-Jonathan does not soften the law. It specifies the method: "Whoso doeth work upon the Sabbath, dying he shall die, by the casting of stones" (Exodus 31:15).
Stoning, in the Torah's legal system, was the most severe of the four forms of judicial execution (Sanhedrin 49b records the hierarchy). Why did Sabbath desecration warrant it?
What does the stone teach?
The sages saw the punishment as theologically mirrored to the crime. The Sabbath-breaker claims the world is still in motion — that there is no divine pause built into creation. The community's response, in the ancient legal system, was to place stones — the most still, most inert, most ceased things in nature — upon the transgressor. The stones that neither grow nor move answered the person who refused to be still.
But the deeper rabbinic tradition (Makkot 7a, c. 500 CE) recorded a crucial qualification. A court that executed even once in seventy years was called a bloody court. The procedural bar was set so high — witnesses must personally warn the offender, the offender must verbally accept the warning and defy it anyway, two adult male witnesses must see the act simultaneously and from the same vantage — that capital cases became almost impossible to conclude. The Torah's verse sets the weight of the prohibition. The rabbinic system nearly ensured the weight never fell on a living person.
So the law functioned as statement more than sentence. It declared: the Sabbath is as serious as anything in the Torah. And then it built protective fences around ever acting on that declaration, so the community could take the Sabbath with absolute seriousness without becoming cruel.
The Maggid takes this home: some things must be named with the gravest language even when they will never be punished with the gravest hand. The language keeps the thing sacred. The restraint keeps the community human.