This is a very interesting discussion, when I saw it's name, and it's length, I was expecting it to be akin to the average Halo thread, but pleasant surprises are always nice.
First of all, I would like to address physical sovereignty. It doesn't appear that the government as a whole subscribes to that idea in the first place. At one time they did, but currently, there is a rather long list of what you can and cannot do with your own body or to it. You cannot take some drugs, you can be forced to take others, you cannot sell your own organs to others, and even your right to die isn't absolute. Sadly, I don't think anyone is truly sovereign over their own bodies with the current laws and boundaries the government currently has.
But for the main point, I don't think men should have a legal say or legal recourse if a woman seeks to terminate a pregnancy. So long as it is legal I feel that it is her choice, since it is her body and the child rearing would be primarily her responsibility and would be so for the next 18 or more years. If she doesn't want it, she has ways out.
Men have their own responsibilities as to the child, and it is primarily financial in most cases. Sure, having a father figure impacts your life greatly, but in most family arrangements he provides the roof over your head, the food on your table and and would do so for the next 18 or more years. If he does not want his responsibility though he is out of luck, he has no ways out. There's no legal recourse, choice or alternatives, it's two decades of financial responsibility taken out of his hands (and let's be honest, most men define themselves by their financial success).
Now, here's a scary thing. The leading cause of death among pregnant women (aside from pregnancy related complications) was murder in the US (for that age range it's usually accidents). And you can bet it's not random strangers doing it in most cases.
I'm not bringing that point up to excuse the behavior in any way, but I think it offers insight into the current state of things. When you take an immature individual who is not ready for any of the responsibilities of life (however they make act), take all control away from them, then force the responsibility on, they'll either grow up or blow up.
So the way I see it is the woman has the child rearing and physical responsibilities of a pregnancy, which she can, if for whatever reasons are necessary, get out of (either through terminating the pregnancy or adoption). While the man has primarily financial responsibilities, which he, for whatever reasons, cannot get out of.
I think it would be only fair to allow him a way out as well. Implementation of any such system though is extraordinarily tricky though. The choice to end a pregnancy or give up a baby is final, while writing a check every month is not quite as concrete. Humans are fickle creatures, you wouldn't want a man saying he'll support the child, then when the time comes he decides that he doesn't want to anymore and can legally say he doesn't want any such responsibility could leave a woman in a real bind.
Honestly, I think you would have to have the parental situation outlined in writing early in the pregnancy, by the time what is going to happen with it, to avoid any trouble.
I would also worry about the societal impact as well, since it is generally beneficial for a child to have two parents, and I don't doubt that if many men had an easy way out as opposed to child support or marriage, they would take it. I somehow doubt that would be a good thing for many children.