I loved this mission, definitely the best ground mission in the game so far! I hope they somehow expand upon the choice you made between who you support, or at the very least have more missions like these.
I chose Drake simply because Section 31 may seem untrustworthy but I think they are a necessary evil in a dangerous galaxy. That, and the fact that the Captain wasn't behaving like a captain should when I questioned him. Also, it didn't make sense if Drake was the Undine. Why would he turn around and board the ship with you, proceed to help you sedate all the crewman, then confront the captain if Drake was the Undine?
I hope this quest will get me recruited into Section 31 down the road, how awesome would that be.