Even without the sewage (and work has restarted on the treatment plant, apparently), I wouldn't choose Nerja. There are many better beaches in Andalucia, including those next to smaller towns or villages where you can stay, potter about and eat. For example along the Atlantic coast such as Bolonia (though sometimes windy), or going further east beyond Almeria city (keep going east and you end up in Murcia, which has great beaches, but too out of the way for your plans!).
However, with your itinerary I would suggest Malaga. By public transport it is easy to get there from Sevilla and also to get from Malaga to Granada (by bus). There are good beaches (might be busy, but you don't say when and Catalonia is also be busy), a nice seaside area along the esplanade, and the city is itself well-worth visiting with the castle, very mini-"Alhambra", Roman theatre and the food-orientated old town part which has been massively improved in recent years. But Malaga is a big city and not a smaller town if that is what you want. I doubt you will find a central hotel with a pool, except perhaps the very posh hotels, but would you need it given the sea is there? There are apartment complexes with pools.
