In accordance with Section 30 of the Education Act (1998), no student can be required to attend instruction in any subject which is contrary to the conscience of the parent of the student. This applies at both primary and post primary levels.
I am not aware of any particular instances where a parent's wishes in relation to religious instruction have been refused by a school. This would be to contravene Section 30 of the Education Act.
My Department is currently drafting the Education (Admission to Schools) Bill. The main objective of the Bill is to provide an over-arching framework to ensure that how schools decide on who is enrolled and who is refused a place in schools is more structured, fair and transparent. However, the Bill will also provide for a school's enrolment policy to include details of the school's arrangements for students who do not want to attend religious instruction.