The points the other posters make (re: diving from a zodiac, tech diving support) are good ones, but to me the thing that makes this not even a question is the experience I had back in January.
I've been to Cocos twice now (both times w/the Undersea Hunter folks). In January we pulled anchor twice to get into search patterns for missing divers from the Aggressor (the good news was that in both cases they were found within 45-75 minutes (one group drifting on the surface, another in one the many bays surrounding Cocos).
Anyone can get separated from the group at Cocos (this is advanced diving - strong currents, chop, and open ocean all play a part here). The difference is that the Undersea Hunter folks always make you dive w/EPIRBS (personal transponders). Before your first dive you're instructed on how to use these, when to turn them on, etc. In short, you get separated on the surface from the panga and no one sees you, you turn it on... it sends out the emergency signal that every boat within x miles (and the ranger station on the island) will pick up. Triangulate the signal, and they can figure out where you are.
At one point I heard the Aggressor was using a similar system, however when we were there in January they weren't, and it showed.
For this reason alone, this isn't even a choice for me. Go with the safer option (this isn't a theoretical, we experienced the implications of not having these twice in 5 days)...
On a less serious note - the panga drivers (like Pepe) on the Sea Hunter/Undersea Hunter boats are literally the best drivers/topside dive staff I've seen anywhere in the world. These guys make diving in difficult situations safe & fun. Go with the best dive staff and the safest dive ops...