For what is worth, I find this scenario nice as it is. My suggestion (since you've asked for it ) would be to add a few red herrings to the mix.
For instance, maybe some Orion pirates who also heard about the subspace weapon testings and want to see if some of them have been left behind. They may be following the crew thinking they retrieved something from their studies, or approach from the other side and be on the tail of the S31 agent (thinking he may known something).
Courd could also have a business rival who could be trying to muddy things - selling Tando's location either to the PCs or to the S31 agent.
Maybe also the pirate will not stop to shooting the Captain and may actively try to further hamper the crew's movements - maybe sending another (unrelated) saboteur on their ship.
Those suggestions aim mainly at befuddling the players and enhance their paranoia, since it seems to be what you like to throw unto them . I don't know if that was what you were looking for ?
"The main difference between Trekkies and Manchester United fans is that Trekkies never trashed a train carriage. So why are the Trekkies the social outcasts?"
Terry Pratchett