Religion and social conventions are aligned in this novel. One reinforces the other, with religion forming the perceived basis for morality and moral action in the general populace. However, this type of conventional morality (and conventional moral reasoning) is shown to be inadequate for dealing with several quite important situations.
One of the novel's most important themes might be stated this way: A truly moral position is only possible when the individuals invovled in a given situation are allowed to be fully seen and fully acknowledged in thier individuality.
Conventions, usually religiously founded, cannot be taken as a final moral standard as they do not account for individual differences in temperment and spirit.
The prevalent social conventions are discarded on at least two very important issues in the novel, as Philotson agrees to allow Sue to leave him and as Jude and Sue raise children together without getting married.
The wrestling over the issue of marriage that takes place in Jude the Obscure is in a larger sense a function of the definition of the self which takes place throughout the nineteenth century.
Challenging religiously-founded conventions is, in its way, a defense of secular values, especially as these values relate to the notion of individuality and individual difference.