An array of submerged "propeller towers" are stationed off the coast of Peru/Equador landward of the deep sea trench. These towers would turn slowly, propelling cool water from about 1000' deep to the surface, thereby cooling some of the surface water and reducing the effects of future El Ninos.
tower would be electrically powered from shore and would be about 500' high with about one propeller every 50 feet. Each propeller would be 20 feet in radius and would turn at a few rpm at max. The highest propeller would be about 50 feet below the sea surface.
The towers would be arranged in "propeller farms", identified by buoys and in GPS maps. The farms would be separated by channels, allowing deep-hulled and submerged vessels to navigate "highways" between the farms.
The idea is to no prevent El Nino, just to take the edge off of it assuming el Ninos become more powerful and longer-lasting in the future.
Just as El Nino has positive and negative effects on weather, the absence of El Nino (or La Nina) also has positive and negative effects. So to completely stop an El Nino would not be good (in addition to being impossible).