Seems to be weird timing to give it the chop, sounds like they put up with losses for a few years. Obviously the route is long/thin and may be sub-economic but everything else would seem to point that conditions may be getting more favourable for this route to remain. The AUD is going down, closer military links between the US and Australia, lower jet fuel prices, possible rebound in Japanese tourism and trade.
At only twice a week it hardly has the appeal for connecting passengers to Japan or indeed the USA, but maybe a bit of advertising and sensible flight timings would have increased its appeal to both Australian and Japanese markets?