Ah, I understand. That's a fairly common reaction to domestic violence matters.
Courts don't generally like cross-applications because it becomes difficult to identify who the perpetrator is if there is a contravention, but am I right to say that your order against him was sought by police, while his order against you was sought by himself?
Remember, a domestic violence order isn't a criminal conviction - it's a precaution to say that if you do contravene, it will turn into a criminal conviction - which is why courts aren't too cautious about ordering them. Kind of a 'Well, if you're contending because you're not a threat, then what difference does it make if the orders are made?'
If you have already opted to contend the amendment, you could accept without admissions (which is basically saying 'I accept these but do not admit to any of the allegations made against me'), or you might consider pitching a mutual undertakings to the court and to the other party that is basically a 'promise on paper' that you won't commit any acts constituting domestic violence against your ex's girlfriend. It is not enforceable by law, but it becomes extremely easy to get a domestic violence order if the undertakings are breached.
In regards to your concerns about it potentially affecting future hearings for parenting matters, that is highly dependent on your individual case - I don't know your story and I don't know his, so there is no way of predicting what impact the allegations might have. In my own experience, I have always found that both parties are equally responsible for the conflict, but neither is ready to really admit it.
However, you will be interested to know that parenting orders only consider domestic violence orders *insofar as is necessary to protect the child from family violence*. What that means is that the Family Court (or, as is more likely in your case, the Federal Circuit Court) will make orders that enable the child to live/spend time with each parent in such a way that they are not in danger. For example, the court might order supervised time with the father, or it might order that the father only spend time with the kids at a contact centre, or it might order nothing of the sort - it might decide domestic violence is not a genuine issue and is just being used as an excuse to frustrate proceedings.
At the bottom line, courts will only make orders in favour of the children's best interests, and it is a very rare occasion when a court will decide it's in the children's best interests never to see one of their parents again.