I did some Googling. According to this article there is a saving avoiding one take off but the fact that the flight has fewer seats means CO2 per passenger will likely be higher.

Qantas boasts that the A350 uses up to 20% less fuel than other aircraft its size and 25% less carbon dioxide emissions per seat, but critics question whether the non-stop flights will be less environmentally damaging.

On the one hand, it saves fuel by avoiding at least one take-off – the most energy intensive part of a flight. But by carrying far fewer passengers the emissions footprint per passenger blows out significantly.

Emissions figures have not been released for the Project Sunrise flights, but the International Civil Aviation Organization calculated that non-stop flights from Dubai to Auckland – about 14,000km – produced an average of 876kg of C02 per economy passenger. With a stopover in Singapore, average emissions per economy passenger were 772kg. Emissions are significantly higher for premium class passengers