Oh Dear. Oh Dear. Oh Dear.
Just had my daughter kneel on the living room floor and put her hands together and start..."Mother Mary I love you", and embark on a big long prayer... Asked her about it and she said teacher showed them how to say it. And all after me having a chat with the teacher and head-master who know my concerns... dear me.
No suprise, they will say they'll accomondate your child, which really means allow her to observe and take part in passive indoctrination. I think the church approach will be futile, verbally tell you what you want to hear and continue as normal.
(aside note: before someone tells you these are Catholic schools... back before the Vatican took control of our schools, when Ireland was under British control, there was no embedded faith formation in the schools, in the past Ireland had real secular education, each religious group did have a prayer-time or none, -source Dialogue Ireland)
I would suggest doing what Puck has done (above) send a letter like the one on the teachdontpreach.ie site to the school's board of management, also contact your local politician explain your problem qoute your rights that are being ignored. Having things in writing is very important as proof of contact that you tried to resolve the problem and agreements made.
As far as I have read the ombudsman will seek proof that you tried everything to resolve the issue before going to them.
If the school has a special-needs teacher, then there's no reason the board couldn't put in place the same solution as in Puck's case, at least you'll be going to them with a solution, and hopefully your child can get back to learning real education.