This isn’t about religion, even if you’re trying to make it about religion. You want to get out of your father’s funeral because it makes you uncomfortable.
Life is full of uncomfortable things, you’ll need to get used to it. There’s thousands of times you’ll need to suck it up and be around people you don’t like because it’s the respectful thing to do.
I’m agnostic, used to be atheist. I thought the same thing. Your fathers funeral, family dinners, respectful times, you’re not “making a stand” you’re being whiney and immature. Atheists celebrate Christmas, go to weddings and funerals. We just sit there silently and respectfully. That’s how we actually want to be viewed outside of a religious context.
Figure out the reason you don’t actually want to go and then learn from it. That’s what growing up is.