I realize this was an LRC piece, and not a submission to the Journal of American Philosophy, but I still think you made this way too blunt.Firstly, I don't think Bob's invocation of the "extreme libertarian position" is relevant, unless he means by this the pure (and thus correct) moral position a consistent libertarian would hold. Libertarianism is about total respect for life and property, but it is not clear how a baby dropped by a stork onto Gene's ship has violated any property rights. It doesn't seem the Reason/Cato/Blockian position on this is a logical extension of a libertarian moral framework in any coherent sense.
First, the extreme libertarian position probably IS to have the legal right to kick the guy off your ship. I'm virtually certain that's what Walter Block (of non-Crash Landing posting privileges) would say.
Second, let's make the analogy closer. Suppose the person coming aboard was certain to go around ripping up the sails, or was so heavy that the ship couldn't get to the original destination. Or suppose the owner of the ship had just watched that early Nicole Kidman movie and was afraid the guy coming aboard was a nutjob.
There are plenty of scenarios where even intuitively, most people would think it OK for the ship owner to kick the person back into the ocean. So then the issue is, is Gene's ideal court going to get inside the person's head and second-guess those motives?
I.e. if you agree that if the owner truly feared for his/her life--maybe the person climbing aboard just had a weird look about him, or kept muttering stuff under his breath--then that makes refusal to bring him aboard OK, then I think you're stuck. Because then everyone can just claim that that was the motivation, and it would be hard in practice to prove otherwise.
If you're just trying to prove most cases of abortion are immoral, that's one thing. (I'm neither agreeing nor disagreeing.) But I don't think you've come close to proving that it would be illegal in a just world.
Bob's next point is, I think, his most constructive. Bob's week Nicole Kidman-watching captain scenario aside (how do irrational fears factor into an objective moral assessment of abortion?), Gene's point that the new passenger cannot "compel you to go anywhere you were not going before" is not perfectly analogous to pregnancy. The handling of an unruly passenger whose presence may tear down sails is less clear than the originally framed situation. And of course a pregnancy might lead the mother to have to change the destination if, say, she intended on pursuing a modeling career but would have to "sail elsewhere" if she had the kid. Per Gene's original framing, a weak case for throwing the passenger off (using the "bugger off" clause) could be made if the very presence of the passenger changed the destination of the ship.
I think such points are ultimately an abuse of a metaphor that is much more subtle. The point is that if you have a human being, you have a reasonable obligation to protect him if he finds himself with no other place to go but your ship. Gene suggests that while you don't have to do whatever the passenger demands, you must at least make sure if you do let him off, you make sure he is safe. That's the essential point. Yes, a baby may "tear up sails", may necessarily rule out certain navigation routes, such as a modeling career in the short run, but a baby is only implicitly asking to live, and after all, it was not actually floating in the ocean, it was borne of the ship itself.
The "all aboard" shout was heard, and a baby heard it and got aboard. It's not that a man's ship sunk exactly, but a man was welcomed on board. The captain may not have intended the welcoming of the passenger, but it is not the passenger's fault he was so welcomed. There may be some inconveniences to the captain, but there must be every reasonable attempt to save the life and balance the danger to the ship and the gravity of the loss to the captain as a result of a possibly different course.
This is almost the same as the policy before Roe v Wade in many states, incidentally. Abortion was outlawed, but there were some special cases in which it was allowed, including when the mother's life was at risk.