Is it permissible to gather worshippers for the Friday prayer in one mosque and close the other mosques at the time of the Friday prayer, given the small number of worshippers in each mosque?

The basic principle is that the Friday prayer should be held in one mosque, and it is not permissible for it to be held in multiple mosques without a need. This is the view of Shafi'i and Ahmad, and the well-known view of Malik and Abu Hanifa. So, if it is possible to gather the worshippers in one mosque, then that is the obligatory course of action, provided that no significant harm results from it, such as dispute and discord.