Is it OK if I present religion in darker tone in a novel?

If you live in the US, you can do whatever you want in this context, and with the rise in the ability to self publish, you don’t need anyone’s approval. Your command of English, although pretty good, proves you’re not a native speaker, so I suspect you might not be American. I can’t speak to your culture.

And just FYI, being a theist dies not necessarily mean that one ascribes to the teachings of an organized religion.

Can do anything you want in fiction although as @canidmajor says, there may be more repression in another country.

Legal? Absolutely. At least in the US.

Will the publisher shy away? It depends. Publishers want to sell stuff that will make them money. Fifty Shades of Gray was utter trash, but it sold a lot.

Controversial books sell, if they are any good. A lousy plot and lousy writing will doom a book.

^^ Unless it’s The Da Vinci Code.

Of course it is legal. What authority would punish you for it? The Spanish Inquisition? I’m sure you’re well outside their jurisdiction.

As to whether you are safe to do it, that depends on whose attention you attract. I don’t think Nikos Kazantzakis had death threats over The Last Temptation (although the film version caught more than a few). But Philip Pullman has already received death threats from Christians over the book he hasn’t even published yet. Who can predict this sort of thing? Religious fanatics are both fickle and not very thorough.

Like others said. Let us know what country you are in. In most civilized and modern countries this is perfectly legal, heck, even quite common.

I don’t believe anything in novel writing is illegal, however, whether or not you can present a concept that is guaranteed to offend a certain audience and whether or not you should are two entirely different subjects.

Phillip Pullman’s trilogy ‘His Dark Materials’ explores essentially the same territory you aspire to and while it’s largely popular and actually received less criticism than Harry Potter, it has its share of Christian hate. A man by the name of William A. Donohue who is with the Catholic league tried to boycott it and the Catholic Herald called it “The stuff of nightmares” and “worthy of the bonfire”.

There is also Barabara Ehrenreich who wrote ‘Nickle and Dimed”, an autobiographical account of her undercover experience as minimum wage employee with three different employers. The novel was heavily regarded as fraud and she received several death threats.

These are just a couple of many instances. What you really need to ask yourself here is what you are able to handle.