Some points:

• This is classic costless analysis. A quarantine would have prevented some transmissions of the disease, but would have severely limited the life quality of those quarantined. It would also have made it more difficult to detect HIV (if having HIV means compulsory quarantine, then if I suspect I have the disease I am less likely to get tested). Any proposal looks good under a benefit analysis; you are supposed to weigh those against the costs.
• This kind of costless analysis is especially beloved by medicine and health professionals, whose only measure of value is health (e.g. their "quality of life" measure is essentially just health integrated over lifespan). I would have hoped rationalists would better recognise the complexity of human value.
• The fact that the quarantine is compulsory ought to give the game away that it's not in the interests of the HIV sufferers. Let's call indefinite compulsory quarantine what it is - prison. It might well be in the interest of the rest of the population for HIV sufferers to be indefinitely imprisoned to stop the spread of the disease, but depending on your ethical theory, it is not obvious that the majority should have their way here.
• "What gives the government the moral right to imprison people on grounds of public health?" and "Why should we trust the government to make wise decisions on this matter?" seem like the default questions to ask, and the post doesn't even begin to address them. See (2) above regarding the deformation professionelle.
• How about instead of quarantine, we had instead tattooed all HIV sufferers across the forehead? This would be a less coercive method of achieving substantially the same result. Yet I'm guessing Cochran wouldn't sign up for that. Can phrases like "rights" and "human dignity" now begin to wend their way into the conversation?

Cochran is fond of calling people dimwits and pinheads, but I have rarely read such a tone-deaf post.