I have not done specifically this, but have shot a bunch in low light and some with candles. You will have blowout on the main kernel of the candle flame, no way around this. This would be my plan with the D750.
1. Find where you're going to do the shot. Bring tape and mark the floor. I would suggest painters tape so it peels up easily. On the floor, using the tape, make an upside down "T" - The top of the T is towards the camera. Reason for the letter is to have each person walk up and put their feet in the T - feet together and toes touching the T.
2. Set up your tripod at the distance you need. Using a flashlight on your test subjects face, set your focus. This way each person can step into the T and you don't have to redo focus each time in such low light.
3. Have the person hold the candle just below the face to try and catch as much light on the face.
4. Use a depth of field calculator and figure out what aperture you need to get everything in focus.
5. Now play with the shutter and ISO to find a happy balance. You might use a remote to trigger the camera so you're not adding any additional wiggle to the camera on the tripod since you will be on a relatively slow shutter speed and your subject will not be completely stationary.
Once you have this dialed in it will be pretty easy to repeat over and over with the stationary tripod and T for subjects to stand in.
When you do shoot, fire off a number of shots. You will not always see the slight blur of their body swaying on the back of your camera.
Finally, check your histogram. Your camera screen will appear brighter than usual with your eyes dilated in the church.
Hope this helps. I know there is a good bit of this your already know, but I figure it's better to cover it all than to assume.