I just add both the author's real name and the alias (and, occasionally, other known aliases if an alias is better known than the real name; Reagan O'Neal, for example, is better known as Robert Jordon but his real name is James Oliver Rigney, Jr.) in the author column. I generally know what aliases an author has used but if I discover one at a later date (or, usually, I discover an author's name is an alias), it takes only a minute to find and update any other instances in my library. If I feel further clarification is needed (which is rarely), I can add it to the Comments and it will show up in the book details pane when I select the book. It's not a big enough deal for me to agonize over.
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