Now I'm not exactly sympathetic to those who would romanticize the South's role in the war, having grown up amongst a not-insubstantial population of such people. But this is fairly loopy. Loomis calls the current nomenclature history written by the losers, and in doing so apparently loses sight of the fact that we should aspire to not let the winners write history either, or indeed, anyone but actual historians. Naming events so as to best capture your political sympathies, however sympathetic they may be, isn't what I'd call "playing fair." Besides, if we'd somehow opted to call the Civil War "The War of the North's Glorious and Just Victory," I don't think it's too much of a stretch to say we might have a fair few more people today questioning the actual justness of the result.
Besides, this argument is pretty silly, just from a semiotic perspective. Names don't warp interpretation of events, but the opposite. It's not like there's a scientific definition of "civil war" as opposed to "rebellion"'; it's hardly unreasonable to call a conflict in which the nation divided in half and fought over a major social issue the former instead of the latter. But even if that weren't the case, no one is extrapolating actual history from the name. "Civil War" now refers to a very specific event, and when you hear the word, you think of the event and work from there. Loomis's concern suggests that there exists a large population with a sophisticated, precise definition of the differences between "civil wars" and "rebellions," but who possesses no prior knowledge of a major historical event that utterly reshaped America and no preconceived notions about the rightness or wrongness of each side's actions. Call me skeptical.
tl;dr: What we call things usually really isn't that important, people. Stop hand-wringing over it.