One of Galdos's most dominant indicators about ideas, beliefs, values, or social institutions in Dona Perfecta is that the religious fervor that dominates the provincial parts of the nation clouds the judgement and prevents restoration from happening.  Galdos constructs a dualism between Madrid and Orbajosa. There is a collision between the values of metropolitan progressive thinking and the reactionary thought that is governed by institutional religion in the small outreaches of Spain.  What Galdos would describe as "the stagnant, stupid, fanatical Spain of the country districts" is governed through a dogmatic approach to religion.  

Dona Perfecta represents this herself in the belief that strict adherence to the institution of religion precludes everything else.  In her understanding, the ideas, beliefs, and values that represent power and a "perfect" sense of truth resides with the institution of the church.  Pepe is diametrically opposed to this. Coming from Madrid and armed with a rather progressive approach, he espouses the values and ideals that Dona Perfecta resents.  In having him killed, Dona Perfecta speaks to the orthodox values that lie outside of question and a position where context is not addressed or acknowledged.  The world order that both embrace are mutually exclusive.  His is a more modern one, while hers embraces that traditionalist notion of the good which is guided by the church and strict adherence to the institution of religion.  In Pepe's death, Galdos seems to be suggesting that the tolerance and embrace of truth that lies outside of the institution is not an element that is immediately embraced by all of Spain.  For Galdos, the "stagnant" must overcome its resistance to change and clearly recognize that blind faith to institution of the church is not the path that modern Spain can embrace for progress and advancement.

Galdos creates an orthodox world where there is corruption. Don Inocencio is far from his namesake in the way he galvanizes public opinion against Pepe. Galdos creates an authority figure of the church who has his own agenda that he wishes to advance, coveting Rosario for his own great-nephew Jacinto. Galdos's intent with this inclusion is to generate thought as to what happens when blind faith is placed in the hands of individuals who do not reciprocate it. The intellectual thought and insight that Pepe embraces is nuanced and complex, not something that the reductive and power hungry forces of the church will accept.  

Galdos establishes that Dona Perfecta's blind faith and unquestioning values within the church, elements that sustains her power as well as the structure of control in Orbajosa, are not elements of social advancement.  The ending of the novel depicts a conflict where if there is no change, the hopes for Spain ensuring its place amongst the modern and liberalized nations of the modern setting are fleeting indeed.