What do you do when the religion you believe in happens to believe in things you don't? In particular, when it endorses moral beliefs which you, simply, do not?
A recent example much in the news is San Francisco's proposed ban on ritual circumcision. You don't have to endorse abstract principles about bodily autonomy to feel uncomfortable with the obligation, as any Jewish or Muslim parent who has inflicted it upon his or her child knows. Or you might be quite passionately committed to your Catholicism and simply fail to share its equally passionate absolute restriction on abortion. Or you might be very devoted to your major western religion and just not accept its doctrinal condemnation of homosexuality.
Can you genuinely count yourself as a believer in that religion when you are inclined to reject some of its official beliefs?
There are three basic options. First, you can choose to give up the religion. Second, you can comply with the religion in practice while working on getting yourself to accept its uncomfortable doctrines. And third, you can comply with the religion while working from within on changing the religion itself. Each of these, however, has its virtues and vices.
The first strategy is of course chosen by many, who prefer to leave the religion rather than accept moral principles they find unacceptable. It reflects a kind of integrity, to be sure, but also a certain kind of arrogance, as if you know better than, well, God -- or if not God then the many smart and good people who have transmitted down the generations what they take to be God's word. You may be quite comfortable with your own intelligence and moral sensitivity, but if your religion was good enough for (say) Maimonides or St Thomas Aquinas, ought you really be so quick to give up on it?
The second strategy, in turn, does reflect some humility, insofar as it accepts the possibility that the moral truth might lie in the tradition after all, despite its poor fit with your own no doubt imperfect sensibilities. But for many this strategy just doesn't work. There are many powerful contemporary arguments to be made to permit abortions in some or many instances, for example, or to endorse universal gay rights, and so on. When you bring these arguments to bear against a moral belief whose source may be a mere assertion without argument in an ancient scripture, it is awfully hard -- and not clearly admirable -- to side with the belief rather than with the arguments.
And, indeed, it is impossible to deny that whatever the ultimate origin of the problematic belief, both it and the scripture asserting it have come down to the present day through a long line of human intermediaries -- each of whom is quite fallible in all the usual ways, ranging from the venial (prone to mistakes) to the truly awful (corrupt, deceitful, power-hungry, etc). This leads directly to the third strategy: once you recognize that religious doctrines and scriptures are ultimately in the hands of human beings, then you realize that they may well be malleable in all sorts of ways.
You don't need to be a scholar to see how religions change and evolve. How many different forms or denominations of Judaism are there today, or of Christianity, or of Islam? These evolve for many different reasons -- often over disagreements on doctrine -- but the point is simply that they evolve. You might in fact need to be a scholar to fully appreciate that ancient forms of each of these religions bear surprisingly little resemblance to the diverse assortment of contemporary forms, but the point is the same: religions change and evolve. They change and evolve when the human beings who espouse them drive those changes. And such human beings could well include you, with your dissonant moral beliefs.
There is, of course, an enormous peril here.
The moment you accept that you may be the driving force for the doctrinal change in your religion is the moment you accept that the official doctrine might not be correct, that it might not be divinely ordained, and so on. It is the moment you accept that nothing, strictly speaking, is actually sacred in the religion's doctrines: if it can err about your issue it can err about any and all others. If you care deeply about your religion, if you believe its authority must ultimately and absolutely derive from God, then this is a very dangerous thing to accept.
But it is a danger that you must embrace.