One engine down shouldn't be too much of a problem. All 4 engines run generators that connect to the ship's electrical bus just like generators at a municipal power station, and the azipod propellers run off that bus as does the lighting, AC etc.. It's like an airplane, there is more engine power available than needed, so you should be able to plug along as normal.
Even if you had made it to Cairns, with rough weather the reef would have been hard to see with all the sand and muck being stirred up. A day trip from Cairns goes to Green Island which doesn't have a lot of coral and fish. The really good part of the reef is quite a ways away and you should really spend a couple of days at one of the good diving & snorkeling locations.