are laser pens (like the sort we used to use in the classroom) really powerful enough to reach an aircraft a couple of thousand feet up?
Yes, except they are not the 'classroom' type. There are different classes and power ratings for lasers, to very different effect. You might find this enlightening:
http://www.pangolin.com/faa/laser-ai...xplanation.htm
Now if you look at the examples, note near the bottom what a 5mW laser at 350ft can do to your view. Sure, 5mW is a low powered classroom style pointer, and 350ft isn't the kind of distance these attacks (and that's what they are) are operating at.
However, I direct you to places like
http://www.wickedlasers.com where you have lasers powerful enough to light matches, pop balloons, etc. Notice you can buy, and very legally in most countries (Australia have now declared all class 3 and 4 lasers illegal, classed as a weapon; class 1 and 2 remain legal and most classroom pointers are class 2) the products on this website. Now notice just how powerful a laser you can buy from placed like wikidlasers. You can buy a 635nm red 500mW (!) laser for a small amount of thousands.
Granted, you'd need some kind of guidance/mounted system to keep the laser trained on a cockpit (impossible to achieve anything more than flashes over the window at any distance with just the hand), but I submit that for a relatively small sum of cash, such a system could be fairly easily implemented.
So, in answer to your question, yes, this can be a huge issue, and could be even worse with a little research and the right know how. And of course, such equipment is so small and trivial to pack away, that by the time the police are even aware there's a problem, the attackers are long gone.