I very much doubt the NRL rule has any impact on the enforceability of this contract whatsoever, assuming it's actually signed and not just a handshake agreement.
What the NRL could do is exercise it's right to refuse to register the contract but the only thing that would result in if each party refuses to concede, is that young Milford would be ineligible to play NRL next season until the contract situation impasse was resolved. If the NRL simply refuse to register a lawful contract because of Canberra complaining, they are going to find themselves potentially liable both to Milford and likely the Broncos.
Milford signing any other contract until the previously signed Broncos contract (assuming it does exist) is mutually terminated would more than likely be deemed to be a breach of contract and NRL has no say in that whatsoever. The NRL is a business, not a tribunal of fact of any kind and it has no legal authority whatsoever to deny or refuse contracts between clubs or players. It does have the legal right to refuse to register the contract, but that is a separate matter to the lawfulness or otherwise of the contract.
If the Broncos have a signed contract for 2015 with Milford and unless they agree to mutually end it, they are well within their rights to enforce the terms of said contract. Whether they would see a benefit in enforcing their contractual rights (ie: forcing him to play or sit out the season, as Canberra has done this year) if Milford signs elsewhere is again a different topic.