These sites should be protected with all care, concern and seriousness of those practices which we have to adopt in areas resided by rural poor. Both Heritage structures and homes of rural poor are very important but highly neglected, and require protection from natural calamities / hazards.
in terms of rain protection, on condition your site is not too large you might care to look at the protective measures introduced on the Turkish site of Catal Huyek which has attempted to address these issues.