Well if you can take a profound philosophical idea that many people disagree with for a variety of logical and emotional reasons, and make them instantly accept it with a couple of sentences, I think there are a good many politicians, religious leaders, advertising executives, and many others who would like to hear how you did it. If I knew how to do that, I wouldn't be here posting, I'd be out either saving the world or making myself emperor.
Realistically, I think you have 3 choices:
(a) Present your controversial philosophical position forcefully and accept that many readers will reject it. Depending on how much they care, etc, people might be grossly offended, or they might simply find your story implausible because it's based on this premise that they are quite sure is false. They may throw your book away when they get to that point, read on to learn what the opposition is saying, or try to have you arrested for hate speech, heresy, corrupting the youth, or whatever.
(b) Actively try to persuade the reader that your philosophical position is correct. If your goal is to convert people to your beliefs, presumably this is what you want to do. Otherwise ... realistically, people have been arguing about these ideas for thousands of years. Unless you have some potent new argument, it's unlikely you're going to change many minds.
(c) Present your controversial philosophical position mildly, in the spirit of "you may or may not agree with this but please go along for the sake of the story". For example, I read Greek mythology and find it entertaining even though I am not a pagan and I don't believe in Zeus. Probably mostly because Greek paganism is pretty much dead today and so not a threat to my religious beliefs in any real way. I've read many books by atheists that express ideas that conflict with my beliefs but I brush them aside and go on if the story is interesting enough. Controversial ideas can often be presented as a "what if", as in, "what if this idea was true? where would it lead?" You can often get readers to go along with something they disagree with in that vein.
One example that comes to mind: Arthur C Clark's story, "The Nine Billion Names of God". The gist of the story is that a group of monks believe that the purpose of human life is to create a list of all the possible names of God. They've been at this for centuries, but now that computers have been invented, they hire some computer experts to program a computer to do this and finish the job in hours instead of millennia. SPOILER* When the computer finishes, the stars start disappearing. Well I don't believe in the religious ideas in this story at all. But I had no problem going along with it as an amusing story. Of course I don't believe that anything like this was true for a moment. So what, it's just a story. I was on another forum where an atheist insisted on trying to re-interpret the story to fit an atheist view, and I thought it was just silly. Clearly the point of the story was that the universe really did end because the monks had completed their task. And OF COURSE that doesn't prove anything about the real world -- either that there is a God or that the universe would end that way. But for some reason this atheist found the idea of a fiction story that contradicted his beliefs so disturbing that he had to find a way to re-interpret it. I think that's even crazier then calling for it to be censored. At least the censor isn't trying to put his own words in the author's mouth.
On the other hand, consider Dan Brown's "Da Vinci Code". This wasn't just a clever story based on a fanciful premise that happened to conflict with many people's religious beliefs. It was a deliberate attack on those beliefs. Some responded by ignoring the book and others by attacking it. But I doubt many Christians read it saying, "yeah, amusing premise, what if".