Say you are going around 45 when the light infront of you just turns yellow. You can stomp on the brakes hard and stop just infront of the intersection or you can floor the car and just barely clear the intersection as the light turns to red and you are at ~60mph...

In the context of hypermiling, which is the more energy efficient decision?

In the first case most of your momentum goes away as heat generated by the brakes, some is saved by the regenerative brakes, and then you have to accelerate back up to speed again as all the momentum has been lost.
In the second case, you eat up a lot of energy accelerating for about 2 seconds, but then you can glide efficiently back to the original speed and don't loose any momentum over case 1...

So, which is more efficient?

From purely an MPG point of view I believe accelerating then gliding is more efficient then stop and start, HOWEVER there is a huge safety issue to consider and I would never recommend gunning it at any light.