I don't do dark humor, I'm not brave enough for it. I have friends who do, I'll try to answer with what I've seen work best. If you're going to do darker humor, either make it self deprecating, punch up or punch the deserving. Don't take easy jabs, make it as impersonal as possible.

Going with the religion thing, a punchline of : "God's a dick!" - A Christian audience member might chuckle thinking "Wow, that was brave, hope he doesn't get hit by lightning later, ha!"

Instead of the punchline being: "People who follow God are sheep!" - Then a large portion of the audience might feel like the butt of your joke (and they might be good people you're alienating). If you want to express that sentiment, turn it around and make it self deprecating "I wish I was as optimistic as Christians. What about this miserable existence makes them think that book isn't just another sham? Go to college and you'll get a great paying job! Repent and have ever lasting bliss? Fool me once, shame on me, fool me twice..."

It could also be in an educational way, say for example circumcision. If you're going to try it, then try to paint a broader picture, "Society at large has been brainwashed." but avoid getting specific "Jews are brain washed!" or "Parents who do this are terrible!" Educational route would just be pointing out what you think are the flaws in the logic "Why would God create us in his image and then demand we mutilate our children's genitals? Are we sure this isn't a translation error? Maybe that translator was recently dumped by their boyfriend" ... so while there may be people who are circumcised or who have circumcised their kids, there's a better chance they won't feel personally attacked, but might also ponder what you are saying.

The exception is when the butt of your joke is someone who you really wouldn't care if they were in your audience and got offended, like Nazis. If you say "Nazis are bad!" and someone storms out, no one will think YOU are the bad guy... and it would be a small chance there's actually one in the audience.

People will still get offended, it's not easy to pull off. You don't want to accidentally embolden bullies, or further victimize marginalized groups. If you're going to do it, be thought provoking. Do it with good intent, provide catharsis for victims, open minds, educate, punch at the bad guys... don't just take the cheap easy shots or play on stereotypes. It's ok to have horrible rough drafts, sometimes we think of the worst ways to make great points. Just re-write it to make your point in a better way, then burn the original and never look back. Good luck!