caste system and its requirements are on full display between Ammu and Velutha. Religion is important in the novel in that it shows how it can be twisted and corrupted, used for evil such as lashing out at others or oppressing people in a different caste—but if wielded properly, such as by Father Mulligan, it is a benevolent agent.

Kerala, the setting of the novel, is one of the oldest Christian regions in the world.  Since much of Roy's focus is showing the contradictory forces at work in the area, religion plays significantly into the paradoxical combination of forces at work.  Roy is most obviously criticizing the caste system, which is at odds with both Christianity and communism.  Ammu's family is for the most part Catholic, but they honor the caste system that treats paravans as subhumans, who should walk backwards so that they can sweep their footprints away.

Roy explains why the Communist party was successful in the Christian populated Kerala.

There were several competing theories.  One was that it had to do with the large population of Christians in the state . . .Structurally--the argument went--Marxism was a smple substitute for Christianity.  Replace God with Marx, Satan with the bourgeouisie, Heaven with a classless society, the Church with the party, and the form and purpose of the journey remained similar.

The trouble with this theory was that in Kerala the Syrian Christians were, by and large, the wealthy, estate-owning (pickle factory-running), feudal lords, for whom communism represented a fate worse than death.

Roy goes on to explain a better theory:  as long as communism did not upset the traditional caste system, it was allowed into the region.  Both communism and Christianity were tolerant of the caste system.  We see throughout the novel that Christians and communism are both part of the machine that ultimately crushes Velutha, the Untouchable.

One of the first instances that religion becomes a factor in the story is when Baby Kochamma falls in love with Father Mulligan, a Catholic Priest, and moves to the convent in order to be closer to him.  She eventually looks for a way out since convent life and the food do not agree with her, but it creates a conflict in her family as her father then believes that no one will propose to marry her so he must send her away to America.

In general, however, the book is dealing much more with the conflict of social classes and structure including the problems with the untouchables in Indian society and interactions between them and touchables than it is with religion.  The social considerations and political conflicts including that of the communist community versus the rest of the community overshadow any religious themes or questions in the novel.

I would say that Roy places a great deal of weight on how the social stratification of a nation can impact its people.  The divisions caused by race, class, and religion are ones that occupy important roles in the novel because they help to isolate individuals from fully understanding one another.  The notion of individuals being "trapped," precluding them from fully embracing the condition of another is something that is brought out in the novel.  This is brought on by the social stratification that lock individuals into roles that define their identity.  When the upholding of the caste system prompts a father to kill his son, or when social transgressions reveal the harshest of punishments, the structures that demand such adherence are critical to individual identity.  It is to this extent that Roy depicts race, class, caste, and religion as vitally important elements that define individuals and in doing so, raises the point that perhaps this structure needs to change.

Since caste and class are related in the novel, I will answer both together.  The novel concerns a couple, Ammu and Velutha, who break the Love Laws--a touchable Ammu (upper class/higher caste) falls in love with an untouchable Velutha (low class/ casteless).  Roy portrays this relationship with vivid detail, showing their physical and emotional love.  This relation is taboo in the Indian society of Kerala where the novel takes place, so much so that when Velutha's father finds out about the affair, he offers to kill his own son.  Ammu ends up as an outcast from her family and town as a result of this relationship, and Veluthah is beaten fatally by police officers, who know that they can use excessive force because Velutha is an untouchable. 

In the poignant ending of the novel, we see what a beautiful love Velutha and Ammu might have shared with each other had the caste system been ignored by the society in which they lived.  Instead, their moments of love cost them everything, including the childhoods of Rahel and Estha, who loved both their mother Ammu and Velutha. 

If you compare this relationship to those that stayed within the confines of the Love Laws, you will see the harsh critique that Roy is making of the caste system.  She shows a horribly abusive relationship between Mammachi and Papachi, a marriage that is sanctioned by society.  And, we see the deadening impact of a loveless life on an individual through Baby Kochama.  Neither seem viable alternatives to the love between Velutha and Ammu. 

The elements you have highlighted are inextricably intertwined with the themes of the novel. Note how one of the central plot elements, the affair between Ammu and Velutha, breaks so many taboos. One of the interesting stylistic aspects of Roy's writing in this great novel is her use of repetition of set phrases. One of these phrases that is echoed throughout the novel is first found at the end of Chapter 1 when the narrator discusses when "it all began" and comes up with a number of different responses, finally concluding with the statement:

That it really began in the days when the Love Laws were made. The laws that lay down who should be loved, and how.
And how much.

Note how this important theme relates deeply to your question. This novel concerns the transgressing of these "Love Laws" that are of course built around race, caste and religion, and how these acts of transgression are censured and punished by society at large, whose job it is to maintain those love laws. Thus it is the father of Velutha that actually betrays his son, because he is so shocked and disgusted at his son having a relationship with an upper-caste woman. However, we would be wrong to focus solely on Velutha and Ammu, for Estha and Rahel, in their incestuous relationship, equally trangress these "Love Laws."