I've been on both sides of that one, although currently our church is not doing a program. Just some thoughts from what I've seen:
1. Be sure you have insurance! If your church has a school with an athletic program, then a martial arts program would probably fall under that guideline, but you better check on it to be sure. If there was no physical contact, it wouldn't be quite as big of an issue (although still important), but it's tough to teach a decent MA program without contact!
2. Decide on your goal for the program and keep it in focus. Is it for the youth at your church already? Is it an outreach ministry, where you invite youth from the community to be a part of it? Is it a seasonal class, i.e. dismissed during the summer?
3. Be sure you have the right equipment. As I'm sure you know, most insurance companies will require basic safety equipment, i.e. floor pads, sparring gear, etc.
4. Did I mention insurance?
5. Determine how the program is to be funded. If the students pay for it, since actual services are rendered, it is not considered a donation. Finances are a touchy thing when dealing with tax exempt organizations: make a mistake in this area, and your church could lose its 501(c)3 status.
6. Who has the oversight of the program? If it is accredited by an organization/school, how much control will that organization have over the operations? All that is done through the church should have the oversight of the pastor in some way -- don't do anything that he doesn't want!
7. Be sure you have insurance coverage -- your school's insurance company may not cover you teaching at another location -- people are sue-happy; don't be a victim!
OK, I think I've covered the basics that I would consider. As far as running the class itself, well, I think you've probably got that covered!
Hope that helps...
Salute
edit: YES...That post finally gave me a yellow belt! Now the real work begins...