It's not energy that causes injuries, it's force. But force is much much more difficult to calculate. You need to know the area of the impact, and even harder is calculating how long the deceleration takes.
The helmet spreads out the area so that it's basically half of the entire head (instead of a small area). The foam inside spreads out the deceleration time. The nature of a spring would also slow down (i.e. increase) the deceleration time.
If he body moved backward as it got hit, that too would spread out the deceleration (i.e. move it from his head/brain, into his entire body).
Edit: by way of full disclosure, I wrote the article.
However, a champion boxer hits at ~90MPH. You can't jerk yourself back fast enough to make an appriciable dent on the KE of the punch. The effect is almost all in the dt of F=dp/dt.
Energy is the integral of force times distance (uh, dot-product there: ∫F⃗·dx⃗, where x⃗ is position). The distance should be pretty easy to put bounds on: no substantial force was being applied to the spring until it made contact with the helmet, and after that it, and the helmet, and the driver, deformed until the energy of the impact was transferred into some form other than the kinetic energy of the spring moving into the helmet. That lets you put a lower bound on the force. (Of course it doesn't allow you to put an upper bound on it.)
The thing is that it is not the open cockpit that can kill, it is the speed. And the speed is why this sport has so many fans.
Also remember that apart from being hit in his head Massa also hit a wall of tires at 200+ kph. I know they were there to absorb the shock, still, try doing that in a regular car...
Is a Formula 1 car any better in an impact than a modern car with, say, 5 Euro NCAP stars? I had a quick Google and it seems that the most important safety feature in this situation is the head and neck support system:
"The leading causes of death in auto racing accidents are skull and neck fractures resulting from rapid deceleration during accidents. The Head and Neck Support system (HANS) was designed to reduce these whiplash effects. The system consists of a collar that is attached to the safety belt and strapped to the helmet to hold the helmet in place during an accident. HANS usage became mandatory in Formula One racing in 2003." 
cp eg here: http://www.formula1.com/inside_f1/understanding_the_sport/52...
a) F1 drivers are very fit as opposed to regular people (so they can endure damage more easily)
b) you wouldn't want to drive an F1 on the street because of other safety issues
yeah these days, risk of fire is quite less but still its a delicate balance which one has is more risky (fire or debris hitting drivers)
It was a terrifying accident.
This would obviously depend a lot on the orientation of the spring when it impacted the helmet, but there's a good possibility that the outcome would have been very different if he'd been hit by an object of similar mass but different geometry.
That isn't to say the impact wasn't incredible and horrific. I'm very glad that he appears to be recovering well.
My guess is that more damage was done by the head-on collision with the wall than by the errant spring. These cars have cockpits specifically designed for safety, but without an airbag there isn't much to help the driver in a head on collision with no deflection. The tire wall seems to have absorbed a lot of the energy, but as the car actually penetrated the wall it may have defeated the primary head on collision safety feature, the crumple zone.
Given that the medical treatment Massa has received all seems to relate to head/eye trauma I think it's pretty safe to say it's the spring that did the damage. Kovalainen's impact into the tires last year was similar and he pretty much walked away from that.
> but without an airbag there isn't much to help the driver in a head on collision with no deflection
That's specifically what the HANS device is for, it's a huge amount of help in that situation.
Ruben's lost a spring on his car, and it ended up in Massa's helmet. What the chances of that?
The injury was due to the spring (although the crash didn't help)
If anyone wants to see a demonstration of how F1 car is safe have a look at this: http://www.youtube.com/watch?v=MZqBbLyp6oo Kubica was pretty much on his legs the same day.
The teams are all very concerned about safety and I expect much stronger helmets and visors in the near future. The fact that he walked away without any broken bones is a testament to the excellent quality of modern F1 safety cells protecting the drivers. Unfortunately this accident could still be the end of Massa's career due to the damage to his eye socket.