Answer

First, even when you set one value against another, it is not clear that the value of life overrides it. The reasoning of "Desecrate one Sabbath for him so that he may keep many Sabbaths" assumes that everything serves the value of the Sabbath. Still, your question is valid even according to that rationale, because if we execute the Sabbath desecrator, we have lost many future Sabbaths of his as well.
Second, even if, when they are weighed against each other, the value of life does override, that still does not mean we would not impose the death penalty on one who desecrates the Sabbath. That itself will lead to many other people observing the Sabbath and will deter people, including the person himself, from desecrating it. Indeed, the Mishnah in Makkot says that the religious court would almost never execute people, meaning that this was only for deterrence. About that itself one could say: desecrate one Sabbath, that is, kill one person, so that many Sabbaths will be observed. See Maimonides, Laws of Rebels 2:4.