I think I'm missing something. Jim Henley seems to be claiming that the Lockean notion of rights was somehow convenient for and enabling of European conquest of the Americas. He starts off quoting Locke's claim of a property right originating by mixing one's labor with unclaimed land. He then states:

This particular view of (real) property claims was very convenient to the Age of Colonization, since it gave Euro-originating settlers the opportunity to “mix their labor” with “something not already anyone’s property,” which is to say, land that was sustaining non-Europeans.

But I don't see the connection. The Lockean notion of property rights was very inconvenient for some European settlers. William Penn felt the need to negotiate for clear title with every indigenous community occupying his intended colony. This often included settling competing claims between multiple indigenous communities by buying the contested lands multiple times to ensure clear title.

The Lockean establishment of property rights by combining labor with unclaimed natural resources seems to me to be a fine rule. It is neutral with regards to an individual's ancestry or social class. The details can be set forth in a way to favor some particular individuals or class, but this does not appear to be the case in American history. There were a number of indigenous communities that met even the most strict interpretations of mixing labor with land. Many indigenous groups had agriculture and permanent settlements, obvious claims for land rights. Yet, European descendants still stole their land, and with the same rationalization as used for chattel slavery.

What was convenient to the settling Europeans and their descendants was that the indigenous people looked different enough that the Europeans could convince themselves that indigenous Americans were somehow not quite human, and therefore not entitled to any rights. This is the real problem - blatant racism. It has nothing to do with something being wrong with private property rights. By the Lockean notion of natural rights including property rights, many white settlers were clearly in the wrong, unjustly depriving people of life, liberty, and property.

Until we can all understand the root of the problem - treating some people as non-people - we will have seriously limited our ability to make things right and perfect our nation. As Americans we have a sordid history, with many wrongs that need to be corrected, including slavery, Jim Crow, and our treatment of the indigenous people. Unfortunately, how to correct those wrongs is not clear to me. My economic intuition tells me that straight reparations will be a cure far worse than the disease, likewise, just letting bygones be bygones or a token apology does not fit my moral intuition. My fear is that there is no just solution.

If you can figure out a good and just solution, Palestine also needs you.

Update: Kevin Carson has a good take, and I particularly like his quote of Karl Hess:

The truth, of course, is that libertarianism wants to advance principles of property but that it in no way wishes to defend, willy nilly, all property which now is called private.

Much of that property is stolen. Much is of dubious title. All of it is deeply intertwined with an immoral, coercive state system which has condoned, built on, and profited from slavery; has expanded through and exploited a brutal and aggressive imperial and colonial foreign policy, and continues to hold the people in a roughly serf-master relationship to political-economic power concentrations.

Update II: It is probably not clear above - I do not mean to say that Penn had read and adopted Locke's notions before coming to the conclusion to negotiate for clear land titles - this was more a matter of his Quaker beliefs and pragmatism. The Lockean notion of property rights are consistent with Penn's actions, and most likely not original to Locke.