And lived in them

First, even when you compare value to value, it is not clear that the value of life is greater. The reasoning of “one Sabbath is violated” assumes that everything serves the value of the Sabbath. Although your question is correct in this respect as well, since if we killed the Sabbath violator, we have lost many Sabbaths in his future. Second, even if when they are established, the value of life still increases, it does not mean that we will not impose the death penalty on a Sabbath violator. This in itself will bring us many Sabbath observances by other people and will deter people (including himself) from violating the Sabbath. And indeed the Mishnah on Beatings says that almost no people would be killed in the Sabbath, meaning that it is only a deterrent. Regarding this itself, it can be said that we will violate one Sabbath (i.e., we will kill one person) so that they will observe many Sabbaths. See Rambam, Hala Memariam, 2:4.