Is it permissible to design a service village, funded by European and American entities, that includes an old church for renovation in the Nuba Mountains region, a mixed Muslim-Christian area, especially given that the site was planned as a missionary city during the colonial era?

There is no harm in the aforementioned work; rather, it is a righteous deed if the intention behind it is to serve the poor. It is not affected by the fact that it is funded by a non-Islamic entity or by the presence of an old church. If the interest of the Muslim village necessitated the renovation or construction of a church, there would be no harm in that, and proselytization is a separate issue.