The church clerics got the green light from the regional government to remove the nests after they claimed the storks had caused €32,000 worth of damages to the tiled roofs of the church, news site 20 Minutos reports.
Not content with the initial eviction, Alcolea de Cinca's priests put up electrified fences on the church roofing to stop the long-legged birds from coming back.
The ensuing results were anything but benign, as one of the returning storks was badly electrocuted and broke its wing when flying into the church weathervane.
Firemen, the Guardia Civil and environmental protection agents all helped release the bird and took it to the local bird shelter.
Spanish environmental group Ecologistas en Acción condemned the treatment of the protected species.
"The days when storks used to be considered a divine blessing are long gone", wrote bird lover and blogger César Javier Palacios.