Patrick,
our youngest was recently Christened and I can tell you that it will be over before you know it.
With four others being done at the same time the Priest will likely be accommodating (to a point) but will want to keep proceedings moving along....so there will be no time to change settings or say "hold on, sorry one more time".
If you can get to the Church prior to the day at around a similar time to when the Christening is to be held (or early on the day) I would speak directly with the Priest and ask if flash is allowed along with where they are happy for you to stand (behind the oarents on the altar would be ideal (so you can see the baby's face instead of the back of it's head)...but is unlikely.....so it will probably be from the aisle near the front row.
I used my trusty D70 with 18-70 kit lens and SB800 flash and the photos turned out just fine, although I didn't really get the chance to set the camera as I would if I were taking the photos (as we had a family friend fire off the shots with the camera on Aperture Priority and flash set to TTL, with the diffuser on to soften the flash).
If you can get there beforehand I would probably set both camera and flash to manual.
With flash off, find the settings (aperture, shutter and ISO) that give you the desired lighting of the background. Probably with the 50mm and a wide aperture will allow enough light in and allow you to frame everyone in the shot.
Note these settings to be used on the day.
Then I'd turn the flash on and in manual
mode start at 1/16th and fire off a shot (with a subject standing near the font) and see how this lights them up, and what shadows are created - ask Priest BEFORE doing this...LOL. Then adjust flash output accordingly until you are happy with the subjects lighting.
On the day, you should be able to set the camera and flash to the settings above and you will be free to focus on framing and taking the photos at the appropriate times (during the blessing, during the crying etc.). The Priest may also allow a quick group photo at the font before moving on to the next family....or may be happy to take a few photos after the service.
It will go very quickly so above all, being as prepared as possible is the key!
Also, make sure you're up there and ready as soon as the previous family are finishing so others in the family you're photographing for don't get in your way (with their P&S cameras).
Hope this helps...
Dave