Certainly marginal cost is a lower limit, and microeconomics tells us that in the long term, competition will drive price to equal marginal cost. However, these new drugs are not even remotely close to the "long term" yet. Rather, these drugs are priced to match a customers' "willingness to pay" at a level that maximizes profit. Microeconomically speaking, this is monopoly pricing since at this early stage of a product's life, there are few to no competitors. It is the ability to skim this surplus profit during the period between pure monopoly pricing and pure competitive pricing that usually spurs people to do new and innovative "stuff."
So, who out there is really willing to pay $250K/year? Are there really that many super-rich people out there who can afford this? Well, from the 3rd paragraph in the article, obviously not. Most people who get these drugs have insurance. It's the insurance company that really is the first line when it comes to willingness to pay. Why will an insurance company pay a certain amount of money for an expensive drug? Well at the core, an insurance company will pay if its subscribers are willing to pay the shared cost of the drug to counterbalance the risk of their needing the drug. But also, in most circumstances, if the drug is approved by the FDA for a given live-saving purpose, insurance companies will be required to pay for it, and thus subscribers will also be required to pay for the shared cost of the drug. Under these circumstances, it seems that an insurance company would end up with a price that would be a combination of several factors:
- Cost that subscribers are willing/able to bear
- Cost to put up hoops to make subscribers jump through to get the drug
- Including the related cost of bad press, government sanctions, etc...
- Including the related cost of bad press, government sanctions, etc...
- Cost of alternative treatments with similar efficacy
- Level where reasonable third parties (e.g. voters/government officials) would consider the drug companies to be charging an unreasonable price
Well, I did some google searches and pulled up some OECD (Organization for Economic Co-operation and Development. Prof. Azis, my macroeconomics professor, called it the "club of rich countries.") data about health care spending. Let's take a look at how much we spend and how long we live compared to other developed countries:

Well, from this data it looks like we spent a lot more money than anyone else, but aren't really buying much (or any) life. Now, there are other data axes that I'm not examining. For instance, most of the spending in the US is private (e.g. individuals or insurance companies), whereas in most other countries (which have nationalized healthcare), the majority is public (e.g. government). These expenditures also include elective procedures (e.g. cosmetic surgeries, sports injuries), which are also more prevalent in the US than elsewhere.
Why is this the case? Well, that's a complex issue. There are many policy arguments over this data, and I don't really know how conclusive any of it is, since this topic is heavily politicized. I do recall one guest on NPR a few weeks back talking about this subject. I can't remember who it was, but she looked over spending, life expectancy, and customer satisfaction data across different wealthy nations, especially comparing nationalized health care to the private system we have in the US. Her conclusion was that the reason the data comes out the way it does is because in most European nations, the budget for national healthcare is fixed. Thus, patients whose illnesses have progressed beyond a certain point will no longer receive treatment, and expensive diagnostic technology (like MRI's) are applied in a more judicious manner. This is in contrast to the US, where treatment is typically provided (by an insurance company or by Medicare) for as long as the condition persists or the patient dies.
Recall the second paragraph of the article excerpt where a Belgian study notes the high cost of Herceptin treatment. The implication here (in line with the guest on NPR) is that cost is a factor for whether or not a treatment is adopted for use within the national health care system there. In the US, treatment is dictated primarily by the efficacy of the procedure. Certainly, it's not absolute. Because of the issue of co-pays and off-label usage, there are many situations where an American patient may choose not to receive a certain treatments because the cost is too high. To a large extent, though, it is the entity that bears the smallest fraction of the cost (e.g. the individual with the $30 copay) that makes the decision rather than the entity that bears the largest fraction (e.g. the insurance company or Medicare with the remaning $5000+ bill). Still, who wants to be the person who has to choose who lives and who dies? Isn't it much more comforting to let everyone have their chance, slim as it may be? And politically, who would withstand the cries of hundreds or thousands of widows, widowers, orphans, etc... whose loved ones were denied treatment? In a nation of hundreds of millions, this may seem to be insignificant number, but politically incensed individuals are potent beyond their statistical representation.
And really, what is better? If we need to spend more to save just one, ten, or a hundred lives, who can say that it is or isn't worth it? America is a very wealthy nation with an extremely strong economy. If any nation can shoulder this burden, it is the United States. But of course, there is no easy or definitive solution to this issue. The best I can hope to do is just understand it better.