Whether or not you believe that God exists, or that he owns our bodies, it must be understood that libertarian philosophy only concerns the relationships between mortal men. It does not concern the relationship between men and animals, or men and the earth (insofar as it unrelates to other men). And it absolutely doesn't concern the relationship between men and God.
Don't misunderstand me. What a man does with himself in relation to anything may or may not be God's concern (I believe it is), but the libertarian principle of self-ownership is used to distinguish what men can legitimately do to each other. Not what God can do to man.
This quote by James A. Sadowsky is instructive,
"When we say that one has the right to do certain things we mean this and only this, that it would be immoral for another, alone or in combination, to stop him from doing this by the use of physical force or the threat thereof. We do not mean that any use a man makes of his property within the limits set forth is necessarily a moral use."It really says it all. The purpose of arguing for self-ownership is to understand if the actions of other men are justified. Though God may own our bodies, this fact would not alter the relationship between men. For example, I own a laptop computer. I acquired this through trade. What I traded was legitimately earned, therefore this laptop computer is legitimately my property. It is an extension of myself. If a man named John took my laptop computer without my permission, that would rightly be considered theft and a violation of my property rights to my laptop computer. God only enters the equation if John claims God told him to take the computer from me because it was his will that John have the computer instead of me. Unless God corroborates this claim to me personally, I can rightly consider it theft and a violation of my property rights.
This is how the libertarian principle of self-ownership is applied in the real world. Because I own myself, I own my labor. Because I own my labor, I own whatever it produces, or trades for. The only other alternatives to self-ownership as it concerns the relationships between mortal men, is what Murray Rothbard examined. And they are, "(1) the 'communist' one of Universal and Equal Other-ownership, or (2) Partial Ownership of One Group by Another – a system of rule by one class over another." It is completely irrelevant to this discussion the belief that God owns the bodies of men. What God does with his property are not the actions we're trying to justify. It's what men do with the property (including bodies) of other men that we are concerned with.