perhaps they were having mechanical issues and the boat was unable to move.
If your car broke down in the street blocking a lorry you wouldn't expect it to ram you out of the way.
I don't know enough about Sea Shepard to make an informed post, but if they are fighting to save whales I am all for that. I watched the 'Earthlings' video recently and the way the human race treats animals is disgusting.
The smaller boat was moving under it's own power at the time, or at least moving (the wake behind it shows that), which means that it would have had at least rudimentary directional control.
The Japanese vessel would have had a much harder time trying to avoid it, than the smaller one would the Japanese ship (it takes a rather long time to turn a big, heavy boat).
It wouldn't surprise me if the Sea Shepherd crew put it on a collision course and left it idling on purpose, as IIRC they've tried ramming/intimidating the Japanese ships with their bigger boats, and they constantly try to put their smaller boats in the way of the Japanese boats to get them to change course.
Having watched some of "Whale Wars" I wouldn't trust the crew of the Sea Shepherd on a Peddelo, as their attitude always appears to be rather gung ho, and they don't seem to care about anyones safety.
I think it was the captain who explained they didn't practice launching their small craft because "it's dangerous" (ignoring the fact that the best way to reduce that danger is to practice during good conditions, when they can take their time), and that they didn't want professional sailors* but people with passion, they also put people out in the launches who have zero skills in the minor things like navigating (and indeed they don't necessarily ensure that the person at the helm of the main ship knows what a heading is).
* think that was before they scared of both one of the film crews, and one of the very few experienced sailor.