In the Baptist church I am a member of, I have complete freedom where to shoot from during baptisms. There are anywhere from 5-15 people being baptised at each baptism and new member service, usually in the evening. I shoot a couple of shots of each person giving their testimony and, of course, several of them coming up out of the water. I provide prints for each of them. CDs and emails, too, if desired.
Shooting handheld with a flash, I find the 24-105 f4L IS works perfectly. I'm typically at a 45 degree angle to the baptism pool and perhaps 15-20 feet away. Having the zoom lets me frame it exactly as I want, while, at the same time, not obstructing the view of those in the sanctuary. The IS helps this oldster considerably!
Of course, if you are shooting in an unfamiliar church, be sure to ask the priest/pastor beforehand what to expect, where to be, and if a flash is permitted or not. These days, with cell phones and point and shoots, I suspect that flashes going off during baptisms is a fairly common occurrance.