I think this program is actually defensible, given the circumstances likely to be present in a school invasion in recent years.
If a gunman ever does invade that school, it's likely that kids will be killed; however, they do have a point that increasing numbers of school-hostage situations are ending violently already. We're seeing murder-suicides more often, for example, where an attacker already intends to kill several students (perhaps as many as possible) before killing himself. The usual police tactics to negotiate a surrender with such an individual are bound to be less effective than under the "traditional" hostage situation where the attacker actually wants something, including a clean getaway. If someone's determined to go down in a blaze of glory and take you with him, the sit-tight option starts to look much less attractive because it doesn't matter if you antagonize him or not.
There's also the prospect that publicizing that this is what students and teachers at this high school are being trained to do will make any prospective hostage-taker with a shred of sense think twice (and maybe pick a more pliant school as a target). Someone with demands is not likely going to be able to get them because there will be no time for negotiations with the police or anyone else. Someone intending a murder-suicide including specific targets might well not be able to get to them, even if he does kill others. Someone intending a random killing spree might get his first few shots off, but likely few or no more. In addition, there is strength in numbers: where one student might never actually rush the gunman alone, for fear that they'd get killed and accomplish nothing, it would be much easier to do so as part of a group, and much easier to do so as a group if they were trained in advance to do so (otherwise it would be pretty darn hard to "organize" on the spot).
The student who noted that it's harder to hit a moving target does in fact have a point. I've fired a gun a few times in my life; not many. It's harder than it looks in movies. Obviously, if the prospective attacker is actually an experienced shooter, things could get very ugly. However, my general sense (sans statistics) is that most of these school invaders really are inexperienced shooters who've simply gotten their hands on guns and are counting on hitting terrified, stationary targets at point-blank range. Former SEALs aren't shooting up high schools. Therefore, there's a real possibility that no one would be killed, and only a few wounded.
Obviously, the media and public opinion are going to make this controversial. There seems to be a tendency to see the death of anyone who fights back as an avoidable death (i.e., something that was the fault of the defender, not the invader) and the death of anyone who doesn't fight back but gets killed anyway as some kind of accident or tragedy, not their fault. In addition, I admit that even I, as a supporter of a program like this, at least in concept, get nervous at the thought of a 14-year-old girl like the one quoted in the article trying to take down a grown gunman; however, in practice, my guess is that it would be more likely some of the bigger boys in the area that would actually try to take the attacker down, and even in seventh grade, there are some that are really starting to fill out their adult frames, and might not be at the kind of physical disadvantage that people are likely thinking. Moreover, I don't think the "sit tight and let the professionals handle it" model has as much appeal as it used to, after some very high-profile failures and a string of cases of murder-suicides where the attacker has no intention of letting others live whether they resist or not, and in fact has no intention of surviving the incident himself.
This is the kind of program where its success or failure will probably depend on the first time it's put to the test. It won't last over time if the first incident goes awry, and it will gain incredible legitimacy if the first test results in nobody killed and only a couple wounded. First impressions will count for everything. I won't hold my breath.