First, it's quite clear given your messages here that you are an atheist, not an agnostic. You may be in denial about this fact, or you may be simply misapplying the term.
You do have every right to be concerned: if the course was merely education of religion, your child would not be singing songs. At least, he wouldn't be singing any more songs than he would about math or science. This leads me to believe that this course is intended for indoctrination and not simply for education.
Now, this brings up the question of whether or not indoctrination is a bad thing. I don't want to get too much into the nitty gritty details about that because it is only bound to upset friends here and isn't likely to do anyone any good anyway.
However, I can summarize the concerns that most atheists have with organized religion: the biggest ones I can think of are the suppression of alternative thinking ("don't think for yourself, we've done that for you"), the exploitation of the poor through psychological tactics such as shaming ("God wants you to give!"), and in what is turning out to be more widespread than a few isolated cases, the sexual exploitation of young children.
Now, there are probably more complaints against organized religion than that, and there are plenty of organizations that do not do any or all of those. But it merely there to illustrate the fact that the problems the typical atheist has with organized religion are not appropriate topics for a seven year old. If you pull him out to protect him from these perceived dangers, there is no way for you to rationalize to him why except "it's for your own good". You can't explain to your child that passing the offering plate without putting an offering in it is an embarrassing thing. He will hear the words, and maybe the individual concepts, but not the social implications of a statement like that.
If you want to make it a real impact, teach him things that actually matter. Teach him how the roman roads made military and commerce transportation possible. Teach him how the aquaducts allowed cities to grow larger than before. Teach him the technological differences between Roman and Viking warships and their relative strengths and weaknesses. These are examples of problems and how they were creatively solved with incredibly restrictive constraints. Those are skills that are massively lacking in modern education, where everyone is so focused on scoring high on tests they forget that they need to learn too.
One final note... when I was 11, my dad and I got up at 6 every morning and read a few pages of A Brief History of Time in the morning. I learned a hell of a lot more about astrophysics and black holes than any 11 year old had business learning, and I loved every minute of it. And it was with my hero. If you take the time to teach him the things he's fired up about, he will not forget it his entire life.