You can already create any tool in wmf labs, and use it as an iframe into any wiki project. This is exactly what the existing tools do (at this point, most of them don't use the new maps service, but they hopefully will very soon). Once done, those tools can be used from wikipedia, as long as they are not used by default - in other words a user has to make an action before the map is loaded. An example would be the little drop down map that you see next to geo coordinates in some articles.

Eventually, if community decides that our maps are good and needed, we will ramp up the number of servers to handle the full wikipedia load and build tools right into wikipedia to show maps in the articles by default.

Also, tile server is already capable of producing GeoJSON for its tiles.  For example, see https://maps.wikimedia.org/osm-intl/7/37/47.json?nogeo (which is the geojson behind this image). The ?nogeo is a debug flag to view the json without all the geo data, thus making it much smaller.

We could also produce the needed geojson data directly from the database, for an area that is different than one tile. It would require some work though.

Thanks!