If you take a church to court, you will have a hard time no matter what they have done. Some judges and juries will simply not rule against a church.

Does that church have a regional bishop or other authority above it? If so, take picture and write to it. Or write to the individual leader of that church. If that doesn’t work, write a letter to the editor.

Did a church need a permit to do that work? If so, check and also inquire if there are any local ordinance about landscaping in a way to flood the property of another.

Send them a certified letter and request they repair damages done. Give them 30 days. If they refuse, take it to small claims and ask for the maximum amount allowed in your state. And take a lot of photos, have them enlarged to 8x 10.

The problem lies in the fact if you want to force the church to make changes to the landscape you will need civil court not small claims, so if the church will not cooperate and change the landscape you will probably need to retain a lawyer

But in general when a land owner intentionally alters the rain run off and that causes damage to your property the land owners are liable for such damage