There are a number of very important religious points that Stowe uses to show the evils of slavery.
First, it is important to note that the context of the novel is rooted in Christianity. Also the novel was published in a Christian culture. Therefore, there is a huge blind-spot when it comes to the Christianity of those who did not fight against slavery. The good masters of the novel are no exceptions. Their moral failings are clear in that they did not speak against slavery.
Second, Eva and Tom are the two most morally flawless characters in the book. They are clear examples of Christ. This can be best seen in that they both died and gave life to others. Eva's death leads to St. Clare's conversion to faith. And Tom's death leads to the escape of Emmeline and Cassy. These points are made clear in that Ophelia says that Eva looks like Jesus, and Tom is compared to Christ carrying the cross.
These points would not have been missed by those of Stowe's day.