Is it permissible to pray over all the deceased in the village—including those who did not pray and disbelievers—to avoid discord and for the sake of calling people to Allah?

The ruling on praying over a person who abandons prayer depends on the scholarly difference of opinion regarding their disbelief (kufr). Whoever considers them a disbeliever does not pray over them, and whoever does not consider them a disbeliever sees no harm in praying over them, with a preference not to pray over them as a punishment for them and a deterrent for others.