So maybe there's hope that you can still be redeemed! :-)
I'd say that if you can write a story that fairly presents multiple points of view on a controversial issue, like religion or politics, you're a rare person, and I applaud you for seriously trying.
I've read lots of stories that involve some controversial question, and it is no mystery at all which side the author is on. The people who agree with him are all intelligent and likable and reasonable, and the people who disagree with him are all either silly stereotypes, complete idiots, or violent extremists.
Every now and then I read a story that gives a fair shake to multiple sides, and I'm impressed. An example that comes to mind is the movie, "Other People's Money". It's a story about an investment banker trying to take over a failing corporation, with the intent of shutting down the company and selling the assets at a profit. In the crucial scene, there is a stockholder's meeting where the president of the company gives a speech about how it is wrong to destroy this company just because fluctuations in the stock market make it so that at this instant the company's assets are worth more than the value of the stock. Then the banker gives a speech about how this company is no longer serving a useful economic purpose, and the best thing to do is to shut it down and sell the assets to other companies that will use them more efficiently. I thought both speeches were well done, the sort of thing that the people on each side might actually say. (And I found it quite surprising that Hollywood would make a movie about such an esoteric subject, never mind one that was intelligent and fair.)
Some ideas on how to be fair to all sides:
Bring up your opponents' strongest arguments, not just their weak ones. I've read many stories -- and plenty of editorials and new stories -- where a spokesman for one side makes 10 arguments, 9 of them strong, solid points and 1 weak, and then they just quote the 1 weak one and talk about it like that was his whole argument.
Avoid the "straw man argument": Don't restate your opponent's argument in a way that leaves out essential points, and then ridicule this sham version of your opponent's argument and pretend that you have refuted his real argument. Take the best statement of an argument, not the weakest.
Make characters from all sides intelligent, likable people. I've read plenty of stories where the characters representing the side the author disagrees with are all stupid, nasty, maybe even violent. The obvious intent is to lead the reader to think of everyone on that side as being like this. When challenged, the author says, "Hey, it's just a story!" and "Surely you don't deny that there are some people on your side like this". The latter, of course, is probably true. Any honest person must admit that there are people who agree with him but who are stupid, nasty, extremists, etc. (Every now and then I'm in a discussion on a forum where someone on my side (of whatever issue) makes a foolish comment, and I cringe at how this makes our side look bad.) This doesn't mean that all characters must be intelligent, likable people. A fiction story typically needs some sort of villain. But you can make some of the Christians likable and some not, some of the atheists likable and some not, etc., rather than everybody on your side is likable and everybody on the other side is obnoxious.
Don't make one side or the other an obvious loser in the debate. I've read stories where there's a debate between two viewpoints, and the person on one side is obviously humiliated and beaten. Well that makes it obvious which side the author is on.
Of course how far you get into philosophical debate depends on the nature of the story. A story that is just two people arguing about religion for the whole book would probably be boring -- though not necessarily, if done well. But you can certainly write an entertaining story that includes scenes where people debate religion, and where those scenes fit into the story and are interesting. But I take it this isn't the issue you're struggling with, so I won't get into that.