You can eliminate (or make more difficult) the Sea Lanes VC by editing a scenario file right now with the release version of the game. The
product page has a link to the Scenario Mod doc. There are two basic things you could do to change things for the VC.
One, you could increase the number of turns needed for Japan to control the Sea Lanes. The SeaLanesScoreNeeded property controls this. It is the number of consecutive months Japan must control a functional Sea Lanes base to win (and defaults to 6). Set it at 10 or 12 to make it harder for Japan (or higher to make it really, really hard).
The second thing you could do would be to eliminate it altogether by converting the Sea Lanes bases into normal bases. Setting the sealane property on the three bases (Espiritu Santo, Fiji, and Samoa) to 0 will turn the victory condition off completely, since there would no longer be any bases Japan could control to trigger it. However, this will tend to reduce the South Pacific to a backwater.
The patch does make the allies more aggressive at retaking them, and should be out very soon.
Thanks,