I think this software would just make superstition more appealing. If it blocked what seemed to be the most important line of a paragraph over and over again, it would probably make a kid insanely curious, to the point where he or she might actively seek out information on what's being censored. This might mean secretly meeting with a Mormon friend at school and "learning" all kinds of "cool" "facts" about god.
As others have said, I think if a secular parent were really worried about their child being brainwashed, the best defense would be to instill a healthy interest in science and skepticism. Keep a Bible and Koran in the house and be sure he/she knows that they are very human books that have spectacular histories as a result of being thought of as divinely inspired. Let them hold the books so they don't think they hold some esoteric value that you're keeping from them.
[ Rant ] Remind them that there were hundreds of different beliefs around at the same time and place that the Bible was written, but for whatever reason(s) the beliefs in the bible just happened to survive longer, and thus inspired many other cults that grew large enough to be considered Religions. Then you can point to the Koran as one example, and all of fragments that Christianity has broken into. Let them know that many new cults pop up even today, but are usually snuffed out before they get a chance to get very strong because people today are much smarter than they were when the major divisions took hold. Let them know that people use certain words in these books as justification for killing and enslaving others, and therefore the books can be dangerous. Let them know that knowledge is the best defense against superstion. [ /rant ]
I'm not 100% sure. 
Poor JS. He gets so much shit.
