I have had the same experience and was appalled by the reaction I got from principal and teacher to board of management when I found out they were teaching my son to recite prayers while I had opt him out of RE class
I just don't think we can realistically do this, the RE is embedded throughout the entire day, also its fair to say that there is some disagreement in the Household over the communion. Neither of us was bought up catholic and we are now both atheists, I feel the work they put into communion is a waste of time and we should look to get him doing something of benefit to his education, My wife feels that we should do nothing that separates him from his friends. Of course its not as black and white as that neither of us wants him singled out and we both want him to be studying real subjects, but we differ over how far to go either way. The communion practice though takes up a lot more time than either of us was aware of.
Their is no realistic school alternative, education apart we feel it is vital for him to attend school with his friends from the village, it would be cruel to separate him from them, but even if we wanted to the nearest educate together school is 10 miles away and we both work, shifts in my case.
It is becoming more and more ridiculous as faith demographics change to force children of non faith parents and different faiths to undergo this sort of education, Time is wasted on things entirely separate from learning and you are required to practice prayers at home! its mad and should be stopped.