Part One of this is that GFO is basically Stock, so the dates of availability for the Balao overall is 1943-02-04 to NULL, while the earliest NavalBase it is available at is Brisbane, 1943-06-01, therefore, if you get it "early", you end up at Brisbane. Part Two is that you were based at Pearl. As such, when you came in, and prior to the tallying of your score and awarding of the Balao, you were assigned your next mission, based out of Pearl, which just so happens to be Empire Waters. This would apply even if your new sub was only available at Holy Loch Scotland. That is the way the game does things. It cannot think nor look ahead. Part Three of this is that hopefully, you are not too much earlier than when the Balao is available at Brisbane, because there might not be mission assignments there. If that is the case, when you do dock, you will be "retired". If you are indeed early, just "stay on patrol" and stop at bases, re-fuel and re-arm, even at Brisbane, but do NOT end patrol until a couple of weeks before 1st of June, 1943. Unless, of course, you do want to retire...
btw, it might be advantageous to go to Japan via Midway, both ways, to make that run...