I am, of course, willing to be convinced otherwise, but it appears that this discussion is largely a tempest in a teapot. 
 
The term "libertarian," for instance, is also used in philosophy of mind to refer to the position that is contrary to determinism. Does this cause any real confusion? Apparently not.  
 
Similarly, the term "individualist," WHEN USED IN A DISCUSSION CONCERNING SYSTEMS OF SOCIAL/POLITICAL ORGANIZATION is widely understood. If someone doesn't understand what it means or what context is being referred to in a particular instance of its usage, you simply explain the term to them.  
 
Your point about the origin of the term "individualist" as being derogatory is a somewhat better one, but, I believe the same can be said of the term "Yankee". Hasn't kept 200 years worth of Americans to using that term in a self-referential and prideful way.

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