You have to be careful with fire alarm systems, they're to protect people and are wired in a way to alert you if there are any problems.
As far as setting off the alarms so the entire building evacuates, removing the wires from a horn/strobe probably won't, by itself, set off the alarms. This kind of problem is rare, but if somewhere else in the building, something is having a problem, there is a slight chance the whole building will go into alarm.
Trouble with the System
The fire alarm system is wired for life-safety. Disconnecting a wire will cause the fire alarm panel to show a yellow trouble light, turn on a local buzzer inside the panel, and display the trouble.
The panel goes one step further and calls your monitoring company to let them know about the trouble.
These actions are performed by the fire alarm control panel so the monitoring company can let the church know about the trouble.
Call the Monitoring Company
Before disconnecting anything, call the monitoring company and ask them to put the system "on test" during the time you're working on the system. Make sure they will not take action to call the church when they receive troubles.
Also, because there is a slim chance of setting off the alarms, place the whole system "on test" with the monitoring company. This is so that while you're working on it, they won't take the action of dispatching the fire department. When the firefighters arrive, it's so embarrassing explaining the work you're doing.
The system should be "on test" the entire time you're on site working on the system. However, don't leave the system "on test" when you're not there. If there's a fire when you're not there, you want the fire department to arrive.
Remember, even when the fire alarm system is on test, fires do happen. Placing the system "on test" means you are responsible to look for fires. If there's a fire, you have to call the fire department yourself.
Your camera is your memory showing how the system was wired. Before disconnecting anything, take many pictures to remind you of exactly how the horn/strobe was wired.
The wires have to go back exactly the way they were, or the horn/strobe won't work. Using a voltmeter to confirm the wiring, however, will get you into trouble. This is because when the alarms in the building sound off, the voltage changes. Instead of using a voltmeter, use the pictures you took to figure out how it was wired.
Disconnecting Puts It in Trouble
When you disconnect the horn/strobe, some of the other horn/strobes are also disconnected.
The trouble light showing up on the panel, showing you that you have disconnected part of the system, isn't a problem; the trouble light showing up on the panel, showing you that you have disconnected part of the system, is a feature. It is reminding you that you've disconnected something.
You can silence the trouble buzzer in the fire alarm control panel, but just leave the wires disconnected to leave the system in trouble. It's your reminder that the system is in trouble. Bypassing the horn/strobe by connecting the black wires together and the red wires together takes away that reminder. While you're on site working on the paneling, just leave the wires loose. I'm a professional, that's what I'd do.
Use that feature to remind you to reconnect the system before leaving the premises. Remember, you've disconnected part of the fire alarm system, you are responsible.
If the work takes more than one day, reconnect the horn/strobe before leaving. Remember, you can always put the system "on test" with the monitoring company, and disconnect the horn/strobe again, when you return to finish the paneling.
Testing the System
Once you've finished the paneling and reconnected the horn/strobe, the whole fire alarm system needs to be tested. Sometimes systems don't work correctly after being disabled and reconnected, you need to confirm that the system works correctly.
Make sure the fire alarm system is "on test" with the monitoring company, and then perform a fire drill. Walk around and make sure all of the horns and strobes in the building make noise and flash during the fire drill.
According to the state fire marshal in Minnesota, "If it ain't on paper, it didn't happen". Make sure everything you did is described on paper, especially the detailed description of the testing.
This paperwork needs to be on file on file at the church. No one is going to read it, unless something goes horribly wrong. Then, the paperwork had better be there.
Is It Legal?
Finally, I don't know what's required where you are, but with a fire alarm system, there are some municipalities and states that require licensed fire alarm companies to perform the disconnecting and reconnecting of devices. Just to keep out of trouble yourself, before disconnecting anything, you will have to find out.