It had no choice.
The Australian Constitution plainly confers legislative power around marriage to the Commonwealth. It does this in Section 51, subsection xxi.
The Australian Constitution says that when the laws of the States (and Territories) conflict with the laws of the Commonwealth, the Commonwealth laws will always prevail.
The Australian Capital Territory enacted legislation allowing same-sex couples to marry, fully knowing that Commonwealth law allows for marriage only between Men and Women. The law was always going to be struck down, and in fact I’d argue it was designed to be struck down in order to bring attention to the cause.
Whatever your opinion on marriage equality, this was always going to happen – from the very moment the bill became a Law.