actually the right to education in australia derives from our treaty obligations under the international covenant on economic, social and cultural rights (specifically articles 13 and 14). it might be thrown around flippantly but without withdrawing from this treaty, the australian government has the positive obligation to ensure that education is accessible.
s 116 of the constitution forbids the government from prohibiting the free exercise of religion. many religions have tenets that exclude and restrict membership and member rights, and they are free to practice their religion as such and so long as they do not contravene the law. what s 116 prohibits is actually quite narrow, and has generally favoured religion, and the relationship between broad-based funding for religious schools and the religious freedoms of those schools is a very complicated issue.
this is all, however, besides the point. public education is available to all students, and for that reason the exclusionary practices of religious schools, based on religious principles, does not infringe on anyone's right to education. furthermore, it is very unlikely that catholic schools could maintain an argument that, based on their religious precepts, they have the freedom to exclude homosexual students.