For obvious reasons, the designers didn't want to seem like they were promoting one religion over others (see their cute little disclaimer on page 77 of the manual--"We're game designers, not theologians."). But it's remarkably easy to play with the levels.
Go into the directory C:\Program Files\Firaxis Games\Sid Meier's Civilization 4\Assets\XML\GameInfo and open up the file "CIV4ReligionInfo." You may need to DL an XML editor depending on what you have installed on your machine.
Anyway, once in the XML document you can alter the values of each religion.