Have you considered flying into a more widely served European city such as Paris (CDG) and then travelling by train to Zagreb?
The 'Seat 61' website has full details: see under 'Croatia' then look at the London to Zagreb information, but in your case starting from Paris. (You could also fly into Frankfurt in Germany).
This way, you could travel from Australia on Philippine Airlines and then using a separate ticket (PNR), on Oman Air to Paris in J for what is often a very good price. AF also now has a MNL to CDG route three nights a week, and has been offering good value fares albeit without lounge access.
Other carriers such as EK/QR are to be wary of, as EK often has 2-3-2 in J (no thanks!) and QR 2-2-2 but without window seat direct access to the aisle, unlike WY that has that very handy feature. I can recommend WY as excellent.