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I can't offer much help on the cleaning and chlorination of wells front, but there are a number of options regarding toilets for areas with high water tables.
firstly, let me recommend Duncan Mara's website which has an enormous amount of information, including stuff about urine diversion toilets: https://www.personal.leeds.ac.uk/~cen6ddm/ See eThekwini latrines and arborloo
The simplest option is by far the arborloo (AKA fosas migratorias) very small pits that are used for a short period, the slab and superstructure are then moved and a fruit tree planted in the back filled pit. There is a good book by Peter Morgan that you can download: https://www.ecosanres.org/ecologicaltoilets.htm which should give lots of ideas. This covers both arborloos and urine diversion options. Composting toilets that do not have urine diversion tend to have a bad reputation. The only justification for going this route is where there is a proven demand for reuse of urine in agriculture and where people are prepared to deal with the compost.
The key factor in all of this is collaboration with the users in deciding on the strategy to be tried and then in the selection of materials and development of the designs.