I don't see how this is a pro-church sort of vibe. Nobody in the churches i grew up in would talk so openly about this sort of thing, and especially not in such a sarcastic manner.
Doubly so since it's a dude wearing it; if being trans is a sin, then joking about it sarcastically is definitely taboo.
I thought the joke was making fun of pat robertson's wild quote "the feminist agenda encourages women to kill their children, practice witchcraft, and become lesbians."
I read the shirt as "sorry missed church /s, i was too busy fucking around with things that are horrible for church-people to bother with it lmao".
I'm gonna guess the shirt is meant as an unironic "Checkmate atheists." Insular social groups tend to forget that the things that they care/feel strongly about might not even be on the collective radar of everyone else - print those things on a shirt and sometimes objective hilarity ensues because it opens the wearer up to outside interpretations that run counter to their intended meaning.
On the other hand, they could be a witchy lesbian, or be showing unironic support for their favorite witchy lesbian in their life. That would be cool, but I'm not betting on it.
Pat Robertson went hard. [The feminist movement] is a socialist, anti-family political movement that encourages women to leave their husbands, kill their children, practice witchcraft, destroy capitalism and become lesbians.
The kill their children part is omitted from humorous re-quotes, but he was being willfully cruel and hyperbolic.