Religion, during Isabella and Ferdinand's reign was held in extreme high regard; however it is unfair to say that Isabella and Ferdinand's policies were motivated solely by religious issues. The Crown did on occasion, place 'spiritual health' above matters considered to be more mundane and conventional - but I believe that there was a lot more than religious issues responsible for their actions.
Isabella was regarded as an extremely religious queen; she viewed religion as truly authentic and pure, she felt it her duty as queen to 'fight Satan in all forms and to rid him of her kingdom'. For more than 250 years, Christianity, Islam, and Judaism coexisted in what was known as Convivencia, however, change was due, as calls grew louder for a crusade against the Muslim kingdom of Granada and of the Mudejars in Castile and Aragon. In 1477, Isabella declared 'All the Jews in my realms are mine and are under my care and protection' - Fifteen years later, they were expelled from Castile and Aragon, this ended several hundred years of Convivencia.
Ferdinand however viewed religion through a 'political eye piece' - meaning that politics was, in his mind, of more importance than that of religion. For the best part, Ferdinand agreed and totally endorsed his wife's strategic tactics, only he had more focus on the political aspects of the policies than the religious side for instance in the crusade against the Muslims in Granada he was more motivated by political and economic gain, rather than religious benefits - Ferdinand was by far a more complete diplomat than Isabella.
Isabella always put religious considerations ahead of economic. The expulsion of Jews and Muslims, and the dispersal of Conversos and Mudejars, especially in Castile, had a poor result on the silk, leather and textile...