Birth control is invariably a hot button political issue. Annoyingly, in this case, actual health issues and the actions of the FDA cannot be wholly dismissed as mere politics any more than the politics aspects can be wished away because of legitimate process issues and medical concerns.
First, it is rather important to recognize that FDA is generally very conservative about over the counter (OTC) drugs. A lot of things that are OTC today are OTC because they are grandfathered. (For example, the court sites the availability of acetaminophine (Tylenol), which is grandfathered OTC by law.) In fact, the FDA has been cutting back on the availability of some drugs (or requiring new warnings) that have long been OTC based on new research.
Legally, the question is whether the Secretary of Health and Human Services (HHS) acted arbitrarily and capriciously in overruling the Administrator of the FDA when the Administrator approved Teva's initial application to distribute Plan B OTC to all ages. The fact that the Secretary rarely exercises this authority, and the fact that the decision had clear political overtones, is not in and of itself grounds for reversal as arbitrary and capricious (although obviously they raise legitimate concerns for review). The standard is still a deferential standard under Chevron. As long as the agency action is not unreasonable, and as long as it did not violate procedure, it must be upheld.
Here, it is not irrational to consider that 11 and 12 year olds who are sexually active (or regularly sexually assaulted) will not follow the instructions on the label. Specifically, whether they will take Plan B in place of standard birth control pills on a regular basis. Consumption of standard birth control pills is monitored by a physician (requires a prescription) precisely because it can have long-term side effects (dangerously high blood pressure being the most common). One may, as a matter of policy, argue that this needs to be weighed against the clear negative health consequences of tenn pregnancy. But that is exactly the sort of substitution of the court's judgment for that of the expert agency that is prohibited by the deferential standard of review.
The other point which gets confused here is the sequence of events. After Secretary Seibelus rejected Teva's application, Teva submitted a modified application for distribution to women 15 and older, this time appending survey evidence demonstrating that women age 15 understand the warnings on the label and will take Plan B in accordance with the label instruction as an emergency contraceptive and not in place of standard contraceptives, such as condoms. Meanwhile, the Citizen Petitioners returned to court to challenge the decision of Secretary Seibelus to deny the first application as failing to comply with the initial remand of the court in 2009. The district court judge then granted judgment to the Citizen Petitioners and issued its order requiring the FDA to make Plan B and all generics OTC within 30 days while the Teva application was still pending.
The FDA approved the revised Teva application during the 30-day period, then filed its appeal and motion for stay. As a legal matter, approval of the second Teva application is not a "response" to the court order. It is not a refusal to obey the court order. Obviously the decision to grant the amended Teva application is intended to influence the outcome of the appeal and of the requested stay of the district court's order. But it is legally a parallel process.
This sort of business goes on pretty regularly in the ad law world. But it only tends to get attention on politically charged issues. This is hardly a surprise. But I could wish that this gets reported better.