Once disabling the submarine then killing the dock guard, the quest becomes active again, preventing you from leaving with the tanker. Since you can't re-enter the submarine, this makes the game impossible to finish.
While actually it's still possible to return to the submarine (using lockpick or blowing up the hatch) and disable it for the second time, it's obviously pointless to let the quest active again.
Saw a new bug report on the wiki:
While actually it's still possible to return to the submarine (using lockpick or blowing up the hatch) and disable it for the second time, it's obviously pointless to let the quest active again.